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Whole genome sequencing (WGS) can help identify transmission of pathogens causing healthcare-associated infections (HAIs). However, the current gold standard of short-read, Illumina-based WGS is labor and time intensive. Given recent improvements in long-read Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a low resource approach providing accurate WGS-pathogen comparison within a time frame allowing for infection prevention and control (IPC) interventions.
Methods:
WGS was prospectively performed on pathogens at increased risk of potential healthcare transmission using the ONT MinION sequencer with R10.4.1 flow cells and Dorado basecaller. Potential transmission was assessed via Ridom SeqSphere+ for core genome multilocus sequence typing and MINTyper for reference-based core genome single nucleotide polymorphisms using previously published cutoff values. The accuracy of our ONT pipeline was determined relative to Illumina.
Results:
Over a six-month period, 242 bacterial isolates from 216 patients were sequenced by a single operator. Compared to the Illumina gold standard, our ONT pipeline achieved a mean identity score of Q60 for assembled genomes, even with a coverage rate as low as 40×. The mean time from initiating DNA extraction to complete analysis was 2 days (IQR 2–3.25 days). We identified five potential transmission clusters comprising 21 isolates (8.7% of sequenced strains). Integrating ONT with epidemiological data, >70% (15/21) of putative transmission cluster isolates originated from patients with potential healthcare transmission links.
Conclusions:
Via a stand-alone ONT pipeline, we detected potentially transmitted HAI pathogens rapidly and accurately, aligning closely with epidemiological data. Our low-resource method has the potential to assist in IPC efforts.
Background: Current epidemiological methods have limitations in identifying transmission of bacteria causing healthcare-associated infections (HAIs). Recent whole genome sequencing (WGS) studies found that genetically related strains can cause HAIs without meeting standard epidemiologic definitions, but these results could not provide data in a timely fashion needed for intervention. Given recent advances in Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a validated ONT pipeline capable of providing accurate WGS-based comparisons of clinical pathogens within a short time frame that would allow for infection control interventions. Method: Using electronic medical record data, we identified potential healthcare acquisition of methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and carbapenem-resistant gram-negative rods. Bacterial genomic DNA was directly extracted from clinical microbiology lab plates. Sequencing was conducted with the ONT MinION sequencer and R10.4.1 flow cell. MINTyper for single nucleotide polymorphism (SNP) calling and Ridom SeqSphere+ for core genome MLST were used to determine genetic relatedness. The main outcome was time from pathogen identification to completed genetic analysis. Result: The weekly workflow, from genomic DNA extraction to complete data analysis, averaged 2.6 days with a standard deviation of 1.3 days. (range: 1 to 6 days). Starting in August 2023, we have sequenced a total of 177 bacterial isolates from 156 unique patients. Isolates came from blood (38%), tissue/wound/body fluid (24%), urinary tract (20%), respiratory tract (16%), and rectal swab (2%). To date, six genetically related clusters have been identified. Three clusters involved ST117 vancomycin-resistant Enterococcus faecium (VREfm), comprising a total of 13 unique patients distributed as 2, 3, and 8 patients in each group, with pairwise SNP differences of 20, 11, and 14. Patients within the same clusters showed epidemiological links through overlapping admissions and temporally shared ICU stays. Additionally, another cluster consisted of five genetically related ST633 Pseudomonas aeruginosa isolates, with a pairwise SNP difference of 57.5. Each patient in this cluster had potential epidemiological links through overlapping admission times, despite the absence of identified shared spaces. The last two clusters involved Klebsiella pneumoniae and Escherichia coli (two cases each), with pairwise SNP differences of 18 and 9, respectively. In both cases, each patient showed potential epidemiological links through overlapping admission times. Conclusion: Our stand-alone ONT pipeline was able to rapidly and accurately detect genetically related AMR pathogens, aligning closely with epidemiological data. Our approach has the potential to assist in the efficient detection and deployment of preventative measures against healthcare-associated infection transmission.
Hydrophobicity, swellability, and dispersion are important properties for organo-montmorillonites (OMnt) and have yet to be fully characterized for all OMnt configurations. The purpose of the present work was to examine the preparation of OMnt from the reaction of Ca2+-montmorillonite (Ca2+-Mnt) with a high concentration of surfactant and to reveal the relevant properties of hydrophobicity and dispersion of the resultant OMnt. A series of OMnt samples were prepared using a small amount of water and cetyltrimethylammonium bromide (CTAB) with a concentration more than the CTAB critical micelle concentration (CMC). The relationship between OMnt microstructure and the hydrophobicity and swellability properties was investigated in detail. The resulting OMnt samples were characterized using powder X-ray diffraction patterns (XRD), Fourier-transform infrared (FTIR) spectroscopy, thermogravimetric and differential thermogravimetry (TG-DTG), water contact angle tests, swelling indices, and transmission electron microscopy (TEM). The addition of CTAB and water in the OMnt preparation affected the OMnt microstructure and properties. An increase in CTAB concentration led to a more ordered arrangement of cetyltrimethylammonium (CTA+) cations in the interlayer space of the OMnt and a large amount of CTA+ cations on the outer surfaces of the OMnt. The swelling indices and the water contact angles of OMnt samples depended on the distribution of the CTAB surfactant on OMnt and the orientation of the surfactant hydrophilic groups on the inner and on the outer surfaces of OMnt. A maximum swelling index of 39 mL/g in xylene was achieved with an average water contact angle of 62.0° ± 2.0° when the amount of CTAB added was 2 times the cation exchange capacity (CEC) of Mnt and the lowest water to dry Mnt mass ratio was 3 during the preparation of OMnt samples. The platelets of OMnt aggregated together in xylene by electrostatic attraction and by hydrophobic interactions.
Somatic symptom disorders (SSD) and functional somatic syndromes (FSS) are often regarded as similar diagnostic constructs; however, whether they exhibit similar clinical outcomes, medical costs, and medication usage patterns has not been examined in nationwide data. Therefore, this study focused on analyzing SSD and four types of FSS (fibromyalgia, chronic fatigue syndrome, irritable bowel syndrome, functional dyspepsia).
Methods
This population-based matched cohort study utilized Taiwan's National Health Insurance (NHI) claims database to investigate the impact of SSD/FSS. The study included 2 615 477 newly diagnosed patients with SSD/FSS and matched comparisons from the NHI beneficiary registry. Healthcare utilization, mortality, medical expenditure, and medication usage were assessed as outcome measures. Statistical analysis involved Cox regression models for hazard ratios, generalized linear models for comparing differences, and adjustment for covariates.
Results
All SSD/FSS showed significantly higher adjusted hazard ratios for psychiatric hospitalization and all-cause hospitalization compared to the control group. All SSD/FSS exhibited significantly higher adjusted hazard ratios for suicide, and SSD was particularly high. All-cause mortality was significantly higher in all SSD/FSS. Medical costs were significantly higher for all SSD/FSS compared to controls. The usage duration of all psychiatric medications and analgesics was significantly higher in SSD/FSS compared to the control group.
Conclusion
All SSD/FSS shared similar clinical outcomes and medical costs. The high hazard ratio for suicide in SSD deserves clinical attention.
Langmuir circulations (LCs) arise through the interaction between the Lagrangian drift of the surface waves and the wind-driven shear layer. Quasi-streamwise vortices (QSVs) also form in the turbulent shear layer next to a flat surface. Both vortical structures manifest themselves by inducing wind-aligned streaks on the surface. In this study, numerical simulations of a stress-driven turbulent shear layer bounded by monochromatic surface waves are conducted to reveal the vortical structures of LCs and QSVs, and their interactions. The LC structure is educed from conditional averaging guided by the signatures of predominant streaks obtained from empirical mode decomposition; the width of the averaged LC pair is found to be comparable to the most unstable wavelength of the Craik–Leibovich equation. Coherent vortical structures (CVSs) are identified using a detection criterion based on local analysis of the velocity-gradient tensor and their topological geometry; QSVs accumulated beneath the windward surface are found to dominate the distribution. Employing the variable-interval spatial average to the identified QSVs further reveals that QSVs tend to form in the edge vicinity of the surface streaks induced by the LCs. The transport budgets of streamwise enstrophy are examined to reveal the interaction. It is found that QSVs perturb the streaks resulting in a localized streamwise gradient of the spanwise velocity, that is, vertical vorticity. The vertical shear tilts the vertical vorticity, therefore enhancing streamwise enstrophy production and the formation of QSVs. The results highlight the differences in the CVSs between the Langmuir turbulence and the wall turbulence.
Aphids exhibit seasonally alternating asexual and sexual reproductive modes. Different morphs are produced throughout the life cycle. To evaluate morph-specific fitness during reproductive switching, holocyclic Sitobion avenae were induced continuously under short light conditions, and development and reproduction were compared in each morph. Seven morphs, including apterous and alate virginoparae, apterous and alate sexuparae, oviparae, males, and fundatrices, were produced during the life cycle. The greatest proportions of sexuparae, oviparae, males, and virginoparae were in the G1, G2, G3, and G4 generations, respectively. Regardless of asexual or sexual morphs, alate morphs exhibited a marked delay in age at maturity compared with that of apterous morphs. Among the alate morphs, males had the longest age at maturity, followed by sexuparae and virginoparae. Among the apterous morphs, sexuparae were older at maturity than the fundatrices, virginoparae, and oviparae. The nymphs of each morph had equal survival potentials. For the same wing morphs, apterous sexuparae and oviparae exhibited substantial delays in the pre-reproductive period and considerable reductions in fecundity, compared with those of apterous virginoparae and fundatrices, whereas alate sexuparae and alate virginoparae had similar fecundity. The seven morphs exhibited Deevey I survivorship throughout the life cycle. These results suggest that sexual production, particularly in males, has short-term development and reproduction costs. The coexistence of sexual and asexual morphs in sexuparae offspring may be regarded as an adaptive strategy for limiting the risk of low fitness in winter.
Composite sweeping-enhanced resolvents, referred to as the ${\boldsymbol {R}}_s^2$ model, are proposed to predict the space–time statistics of large-scale structures in turbulent channel flows. This model incorporates two key mechanisms: (i) eddy damping is introduced to represent random sweeping decorrelation caused by nonlinear forcing, leading to a sweeping-enhanced resolvent ${{\boldsymbol {R}}_s}$; and (ii) the sweeping-enhanced resolvent ${{\boldsymbol {R}}_s}$ is composited into its iterations ${\boldsymbol {R}}_s^2$ to yield non-zero Taylor time microscales. The resulting ${\boldsymbol {R}}_s^2$ model can correctly predict the frequency spectra and two-point cross-spectra of large-scale structures. This model is compared numerically with eddy-viscosity-enhanced resolvent models. The latter are designed to represent energy transfer instead for time decorrelation, and thus underpredict the characteristic decay time scales. The ${\boldsymbol {R}}_s^2$ model correctly yields the characteristic decay time scales in turbulent channel flows.
According to Hamilton's rule, matrilineal-biased investment restrains men in matrilineal societies from maximising their inclusive fitness (the ‘matrilineal puzzle'). A recent hypothesis argues that when women breed communally and share household resources, a man should help his sisters' household, rather than his wife's household, as investment to the later but not the former would be diluted by other unrelated members (Wu et al., 2013). According to this hypothesis, a man is less likely to help on his wife's farm when there are more women reproducing in the wife's household, because on average he would be less related to his wife's household. We used a farm-work observational dataset, that we collected in the matrilineal Mosuo in southwest China, to test this hypothesis. As predicted, high levels of communal breeding by women in his wife's households do predict less effort spent by men on their wife's farm, and communal breeding in men's natal households do not affect whether men help on their natal farms. Thus, communal breeding by women dilutes the inclusive fitness benefits men receive from investment to their wife and children, and may drive the evolution of matrilineal-biased investment by men. These results can help solve the ‘matrilineal puzzle'.
Few studies claimed that dynamic jaw (DJ) mode in Helical TomoTherapy® (HT) could improve the cranio-caudal dose distribution without prolonging the treatment time in treating different types of cancer. Also, studies suggested that DJ with a wider 5 cm field width (FW) could replace fixed jaws (FJ) with 2.5 cm FW to reduce the delivery time with the sustainable plan quality. Yet, the study on breast cancer with supraclavicular fossa (SCF) nodal involvement using DJ mode in HT is limited. This study aims to evaluate the DJ mode retrospectively by comparing their dosimetric quality with normal tissue complication probability (NTCP) of organs at risk and treatment delivery time with FJ mode on treating left-side breast with SCF nodal involvement.
Materials and methods:
All post-mastectomy patients, who had been irradiated for left-side breast with SCF nodal involvement were selected retrospectively in this study. With the same dose constraint and prescription as the treated DJ2.5 plan, two extra plans using DJ mode with 5 cm FW(DJ5.0) and FJ mode with 2.5 cm FW (FJ2.5) were computed for plan comparison.
Results:
No statistical significance was found in all the parameters of PTV and OARs, except for V20 of whole lung. DJ5.0 received V20 in ipsilateral left lung than FJ2.5 and DJ2.5. However, the average delivery time of DJ5.0 was significantly lower than that of DJ2.5 and FJ2.5 by almost 40%.
Conclusions:
No statistical significance was found in those dosimetric and radiobiological parameters among three modes while the delivery time has greatly reduced by using DJ5.0. A shorter treatment time can minimise intra-fractional error and better the patient’s experience during treatment.
To understand why Procapra przewalskii does not show the same white myopathy as sheep in Se-deficient regions and to provide reference for feeding nutrition level of artificial population and selection of wild reintroduction areas in the later period, a Se-deficient model was established. The mineral elements content, physiological and biochemical parameters in blood and serum metabonomics were determined. In the Se-deficient group compared with the control group, the Se content was highly significantly lower (P < 0·01), and the Cu content was significantly higher (P < 0·05). The activity of glutathione peroxidase was significantly lower (P < 0·05), but total superoxide dismutase was significantly higher (P < 0·05). By matching the mass spectrum data of compounds with the Kyoto Encyclopedia of Genes and Genomes (KEGG database), eighty-six types of differential metabolites in the serum were identified. The main metabolic pathways included secondary bile acid biosynthesis, biosynthesis of unsaturated fatty acids and pyrimidine metabolism. Further analysis showed that there were seven different metabolites in pyrimidine metabolism pathway between the two groups. And there was no significant difference in erythrocyte, Hb and total antioxidant capacity between the two groups (P > 0·05). The above results showed that the differential metabolism of substances exhibited complementary functions, thus alleviating some adverse effects and resulting normal activities of P. przewalskii can be carried out under the condition of dietary Se content lower than 0·05 mg/kg.
Almost all hospitals are equipped with air-conditioning systems to provide a comfortable environment for patients and staff. However, the accumulation of dust and moisture within these systems increases the risk of transmission of microbes and have on occasion been associated with outbreaks of infection. Nevertheless, the impact of air-conditioning on the transmission of microorganisms leading to infection remains largely uncertain. We conducted a scoping review to screen systematically the evidence for such an association in the face of the coronavirus disease 2019 epidemic. PubMed, Embase and Web of Science databases were explored for relevant studies addressing microbial contamination of the air, their transmission and association with infectious diseases. The review process yielded 21 publications, 17 of which were cross-sectional studies, three were cohort studies and one case−control study. Our analysis showed that, compared with naturally ventilated areas, microbial loads were significantly lower in air-conditioned areas, but the incidence of infections increased if not properly managed. The use of high-efficiency particulate air (HEPA) filtration not only decreased transmission of airborne bioaerosols and various microorganisms, but also reduced the risk of infections. By contrast, contaminated air-conditioning systems in hospital rooms were associated with a higher risk of patient infection. Cleaning and maintenance of such systems to recommended standards should be performed regularly and where appropriate, the installation of HEPA filters can effectively mitigate microbial contamination in the public areas of hospitals.
Frozen embryo transfer (FET) has been adopted by growing number of reproductive medicine centers due to the improved outcome compared with fresh embryo transfer. However, few studies have focused on the impact of embryo cryopreservation duration on pregnancy-related complications and neonatal birthweight. Thus, a retrospective cohort study including all FET cycles with livebirth deliveries in a university affiliated hospital from May 2010 to September 2017 was conducted. These deliveries were grouped by the cryopreservation duration of the transferred embryo (≤3 months, 4–6 months, 7–12 months, and >12 months). The associations between embryo cryopreservation duration and pregnancy-related complications were evaluated among the groups using multinomial logistic regression. Neonatal birthweight was compared according to the stratification of singletons and multiples using multinomial and multilevel logistic regression, respectively. Among all 12,158 FET cycles, a total of 3864 livebirth deliveries comprising 2995 singletons and 1739 multiples were included. Compared with those within 3 months, women undergoing FET after a cryopreservation time longer than 3 months did not show any increased risk of gestational diabetes mellitus, gestational hypertension, preeclampsia, meconium staining of the amniotic fluid, or preterm birth. Furthermore, the risk of lower birthweight, macrosomia, small-for-gestational-age, or large-for-gestational-age for either singletons or multiples was not affected by long-term cryopreservation. In summary, embryo cryopreservation duration does not have negative effects on pregnancy-related complications or birthweight after FET.
The objective of this study was to analyze differences in birth weight and overweight/obesity in a Shanghai twin cohort. We also wanted to study their association and explore possible risk factors for the discordance of overweight/obesity within twins. This was an internal case–control study designed for twins. The 2012 Shanghai Twin Registration System baseline survey data of a total of 3417 twin pairs were statistically analyzed using SPSS22 software. Results show that the body mass index (BMI) of the Shanghai twin population increased with age. Twins with a high birth weight had a higher BMI and a higher rate of overweight and obesity; 0- to 6-year-old twins, male twins and dizygotic (DZ) twins had higher rates of overweight/obesity than other groups. The greater the discordant birth weight rate of twins, the more obvious the difference in BMI (p < .05). There was a significant difference in overweight/obesity between twins with a relative difference of birth weight ≥15% in DZ twins (p < .05). DZ twins, male twins and 0- to 6-year-old twins were more likely to be discordant in overweight/obese than others. The discordant birth weight within twins was not a risk factor for discordant overweight/obesity. However, attention should be paid to childhood obesity, and appropriate interventions should be made at the appropriate time. Genetics may play an important role in the occurrence and development of overweight/obesity. In conclusion, discordant growth and development in the uterus early in life may not lead to discordant weight development in the future.
Carotenoids are increasingly being implicated to have an important role in brain and eye development. This study aimed to quantify the content and profile of carotenoids in human breast milk, maternal plasma and neonatal umbilical cord plasma in Chengdu, an urban area in Southwest China. In this study, fifty-four healthy mothers were enrolled. Maternal blood, umbilical cord blood, colostrum, transitional milk and mature milk were collected. Concentrations of carotenoids (lutein, zeaxanthin, β-cryptoxanthin, β-carotene and lycopene) were analysed by HPLC. We found that carotenoid concentrations decreased from colostrum to mature milk. Hydrocarbon carotenoids with weaker polarity decreased more than the polar carotenoids. Lycopene concentrations dropped by 99 %, β-carotene by 92 %, β-cryptoxanthin by 83 %, lutein by 32 % and zeaxanthin by 22 %. Lycopene and β-carotene accounted for 70 % of the total carotenoids in colostrum, and lutein predominated amongst carotenoids in transitional milk and mature milk (51–55 %). Carotenoid concentrations in maternal plasma were much higher than that in cord plasma. Lutein predominated in cord plasma. The concentrations of all carotenoids in maternal plasma were correlated with those of cord plasma and human milk. These results are consistent with selective transport mechanisms in the mammary gland related to the polarity of carotenoids, and each carotenoid has its own implications, which may have different priorities in the early life development of infants. These findings may help guide dietary recommendations for carotenoid inclusion in infant formulas.
Lead-free ferroelectric electrocaloric ceramics that could convert electrical energy into heat are the promising candidate for environment-friendly cooling devices. For refrigeration devices, a large temperature change (ΔT) and good temperature stability are required, which are highly related to the phase structure and the applied electric field. In this work, a diffused ferroelectric–paraelectric (FP) phase transition is formed in (K, Na)NbO3 (KNN) by using appropriate composition engineering. The relaxor ferroelectrics in this work present both a large ΔT of 1.24 K and a high ΔT/ΔE of 0.19 K mm/kV. In addition, a wide temperature span exceeds 55 °C at the high electrocaloric effect (ECE) criterion (ΔT ≥ 0.5 K) could also be observed. This work not only opens a new strategy for obtaining high-performance ceramics for refrigeration devices but also extends the application area of the KNN-based lead-free ferroelectrics from sensors, actuators and energy harvesting to solid-state cooling applications.
The present study investigated the association between fibre degradation and the concentration of dissolved molecular hydrogen (H2) in the rumen. Napier grass (NG) silage and corn stover (CS) silage were compared as forages with contrasting structures and degradation patterns. In the first experiment, CS silage had greater 48-h DM, neutral-detergent fibre (NDF) and acid-detergent fibre degradation, and total gas and methane (CH4) volumes, and lower 48-h H2 volume than NG silage in 48-h in vitro incubations. In the second experiment, twenty-four growing beef bulls were fed diets including 55 % (DM basis) NG or CS silages. Bulls fed the CS diet had greater DM intake (DMI), average daily gain, total-tract digestibility of OM and NDF, ruminal dissolved methane (dCH4) concentration and gene copies of protozoa, methanogens, Ruminococcus albus and R. flavefaciens, and had lower ruminal dH2 concentration, and molar proportions of valerate and isovalerate, in comparison with those fed the NG diet. There was a negative correlation between dH2 concentration and NDF digestibility in bulls fed the CS diet, and a lack of relationship between dH2 concentration and NDF digestibility with the NG diet. In summary, the fibre of CS silage was more easily degraded by rumen microorganisms than that of NG silage. Increased dCH4 concentration with the CS diet presumably led to the decreased ruminal dH2 concentration, which may be helpful for fibre degradation and growth of fibrolytic micro-organisms in the rumen.
The Antarctic subglacial drilling rig (ASDR) is designed to recover 105 mm-diameter ice cores up to 1400 m depth and 41.5 mm-diameter bedrock cores up to 2 m in length. In order to ensure safe and convenient drilling, drilling auxiliaries are designed to support fieldwork and servicing. These auxiliaries are subdivided into several systems for power supply, drill tripping in the borehole, ice core and chip processing, and drill servicing and maintenance. The required equipment also includes two generators, a drilling winch with a cable, logging winch with a cable, control desk, pipe handler with a fixed clamp, chip chamber vibrator, centrifuge, emergency devices and fitting and electrical tools. Additionally, several environmental protective measures such as a new liquid-tight casing with a thermal casing shoe and a bailing device for recovering drilling fluid from the borehole were designed. Most of the auxiliaries were tested during the summer of 2018–2019 near Zhongshan Station, East Antarctica while drilling to the bedrock to a depth of 198 m.
Staff surveillance is crucial during the containment phase of a pandemic to help reduce potential healthcare-associated transmission and sustain good staff morale. During an outbreak of SARS-COV-2 with community transmission, our institution used an integrated strategy for early detection and containment of COVID-19 cases among healthcare workers (HCWs).
Methods:
Our strategy comprised 3 key components: (1) enforcing reporting of HCWs with acute respiratory illness (ARI) to our institution’s staff clinic for monitoring; (2) conducting ongoing syndromic surveillance to obtain early warning of potential clusters of COVID-19; and (3) outbreak investigation and management.
Results:
Over a 16-week surveillance period, we detected 14 cases of COVID-19 among HCWs with ARI symptoms. Two of the cases were linked epidemiologically and thus constituted a COVID-19 cluster with intrahospital HCW–HCW transmission; we also detected 1 family cluster and 2 clusters among HCWs who shared accommodation. No transmission to HCWs or patients was detected after containment measures were instituted. Early detection minimized the number of HCWs requiring quarantine, hence preserving continuity of service during an ongoing pandemic.
Conclusions:
An integrated surveillance strategy, outbreak management, and encouraging individual responsibility were successful in early detection of clusters of COVID-19 among HCWs. With ongoing local transmission, vigilance must be maintained for intrahospital spread in nonclinical areas where social mingling of HCWs occurs. Because most individuals with COVID-19 have mild symptoms, addressing presenteeism is crucial to minimize potential staff and patient exposure.
We find that corporate innovation is positively related to board diversity as measured by a multidimensional index. The benefit of board diversity is more pronounced for firms with more complex operations, more experienced boards, and stronger external governance, suggesting that diverse boards have superior advising capacity. We find evidence to suggest that firms with diverse boards engage in more exploratory innovations and develop new technology in unfamiliar areas. As a result, they create a larger number of both most-cited and uncited patents. Finally, of the six different aspects of board diversity, professional diversity matters the most for corporate innovation.