New mutation within a common haplotype is associated with calf muscle weakness in Holsteins

A recessive haplotype resulting in elevated calf mortality but with apparent incomplete penetrance was previously linked to the end of chromosome 16 (78.7-80.7 Mbp). Genotype analysis of 5.6 million Holsteins indicated that the haplotype was common and traced back to 1952, with a key ancestor born in 1984 (HOUSA1964484, Southwind) identified from chip genotypes as homozygous for the suspect haplotype. Sequence data from Southwind (an affected calf) and the sire of the affected calf were scanned for candidate mutations. A missense mutation with a deleterious projected impact at 79,613,592 bp was homozygous in the affected calf and heterozygous in the calf's sire and Southwind. Sequence data available from the Cooperative Dairy DNA Repository for 299 other Holsteins indicated a 97% concordance with the haplotype and an 89% call rate. The exon amino acid sequence appears to be broadly conserved in the CACNA1S gene, and mutations in humans and mice can cause phenotypes of temporary or permanent paralysis analogous to those in calves with the haplotype causing muscle weakness (HMW). Improved methods for using pedigree to track new mutations within existing haplotypes were developed and applied to the haplotypes for both muscle weakness and Holstein cholesterol deficiency (HCD). For HCD, concordance of the gene test with its haplotype status was greatly improved. For both defects, haplotype status was matched to heifer livability records for 558,000 calves. For HMW, only 46 heifers with livability records were homozygous and traced only to Southwind on both sides. Of those, 52% died before 18 mo at an average age of 1.7 ± 1.6 mo, but that death rate may be underestimated if only healthier calves were genotyped. The death rate was 2.4% for noncarriers. Different reporting methods or dominance effects may be needed to include HMW and other partially lethal effects in selection and mating. Direct tests are needed for new mutations within existing common haplotypes because tracking can be difficult even with accurate pedigrees when the original haplotype has a high frequency.

Assessing Clinician Utilization of Next-Generation Antibiotics Against Resistant Gram-Negative Infections in U.S. Hospitals : A Retrospective Cohort Study

BACKGROUND

The U.S. antibiotic market failure has threatened future innovation and supply. Understanding when and why clinicians underutilize recently approved gram-negative antibiotics might help prioritize the patient in future antibiotic development and potential market entry rewards.

OBJECTIVE

To determine use patterns of recently U.S. Food and Drug Administration (FDA)-approved gram-negative antibiotics (ceftazidime-avibactam, ceftolozane-tazobactam, meropenem-vaborbactam, plazomicin, eravacycline, imipenem-relebactam-cilastatin, and cefiderocol) and identify factors associated with their preferential use (over traditional generic agents) in patients with gram-negative infections due to pathogens displaying difficult-to-treat resistance (DTR; that is, resistance to all first-line antibiotics).

DESIGN

Retrospective cohort.

SETTING

619 U.S. hospitals.

PARTICIPANTS

Adult inpatients.

MEASUREMENTS

Quarterly percentage change in antibiotic use was calculated using weighted linear regression. Machine learning selected candidate variables, and mixed models identified factors associated with new (vs. traditional) antibiotic use in DTR infections.

RESULTS

Between quarter 1 of 2016 and quarter 2 of 2021, ceftolozane-tazobactam (approved 2014) and ceftazidime-avibactam (2015) predominated new antibiotic usage whereas subsequently approved gram-negative antibiotics saw relatively sluggish uptake. Among gram-negative infection hospitalizations, 0.7% (2551 [2631 episodes] of 362 142) displayed DTR pathogens. Patients were treated exclusively using traditional agents in 1091 of 2631 DTR episodes (41.5%), including "reserve" antibiotics such as polymyxins, aminoglycosides, and tigecycline in 865 of 1091 episodes (79.3%). Patients with bacteremia and chronic diseases had greater adjusted probabilities and those with do-not-resuscitate status, acute liver failure, and Acinetobacter baumannii complex and other nonpseudomonal nonfermenter pathogens had lower adjusted probabilities of receiving newer (vs. traditional) antibiotics for DTR infections, respectively. Availability of susceptibility testing for new antibiotics increased probability of usage.

LIMITATION

Residual confounding.

CONCLUSION

Despite FDA approval of 7 next-generation gram-negative antibiotics between 2014 and 2019, clinicians still frequently treat resistant gram-negative infections with older, generic antibiotics with suboptimal safety-efficacy profiles. Future antibiotics with innovative mechanisms targeting untapped pathogen niches, widely available susceptibility testing, and evidence demonstrating improved outcomes in resistant infections might enhance utilization.

PRIMARY FUNDING SOURCE

U.S. Food and Drug Administration; NIH Intramural Research Program.

Carbapenem use in extended-spectrum cephalosporin-resistant Enterobacterales infections in US hospitals and influence of IDSA guidance: a retrospective cohort study

BACKGROUND

Disparate and rapidly changing practice recommendations from major professional infectious diseases societies for managing non-severe infections caused by extended-spectrum β-lactamase-producing Enterobacterales might hamper carbapenem stewardship. We aimed to understand the real-world management of extended-spectrum cephalosporin-resistant (ECR) Enterobacterales infections in US hospitals and factors influencing preference for carbapenems over alternative treatments.

METHODS

This retrospective cohort study included adults (aged ≥18 years) admitted to hospital with ECR Enterobacterales infections in the PINC AI database. Antibiotic regimens were assessed during empirical and targeted treatment periods and by infection severity and site. Likelihood of receiving targeted carbapenems over time and before or after initial release of the Infectious Diseases Society of America (IDSA) guidance on Sept 8, 2020, was established with generalised estimating equations controlling for patient, hospital, and temporal confounders.

FINDINGS

Between Jan 1, 2018, and Dec 31, 2021, 30 041 inpatient encounters with ECR Enterobacterales infections were identified at 168 US hospitals, of which 16 006 (53·3%) encounters were in women and 14 035 (46·7%) were in men, with a mean age of 67·3 years (SD 15·1). Although few patients received carbapenems empirically (5324 [17·7%] of 30 041), many did so as targeted treatment (17 518 [58·3%] of 30 041), including subgroups of patients without septic shock (3031 [45·6%] of 6651) and patients with urinary tract infections without septic shock (1845 [46·8%] of 3943) in whom specific narrower-spectrum alternatives were active. Transitions from non-carbapenem to carbapenem antibiotics occurred most often on the day that the ECR phenotype was reported, regardless of illness severity. Carbapenems were the predominant choice to treat ECR Enterobacterales infections over time (adjusted odds ratio 1·00 [95% CI 1·00-1·00]), with no additional immediate change (1·07 [0·95-1·20]) or sustained change (0·99 [0·98-1·00]) after IDSA guidance release.

INTERPRETATION

High carbapenem use in targeting non-severe ECR Enterobacterales infections in US hospitals predates 2020 IDSA guidance and has persisted thereafter. Efforts to increase awareness and implementation of recommendations among clinicians to use carbapenem-sparing alternatives in ECR Enterobacterales infections might decrease global carbapenem selective pressure.

FUNDING

US National Institutes of Health Intramural Research Program, National Institute of Allergy and Infectious Diseases, and US Food and Drug Administration.

Measures and Impact of Caseload Surge During the COVID-19 Pandemic: A Systematic Review

OBJECTIVES

COVID-19 pandemic surges strained hospitals globally. We performed a systematic review to examine measures of pandemic caseload surge and its impact on mortality of hospitalized patients.

DATA SOURCES

PubMed, Embase, and Web of Science.

STUDY SELECTION

English-language studies published between December 1, 2019, and November 22, 2023, which reported the association between pandemic "surge"-related measures and mortality in hospitalized patients.

DATA EXTRACTION

Three authors independently screened studies, extracted data, and assessed individual study risk of bias. We assessed measures of surge qualitatively across included studies. Given multidomain heterogeneity, we semiquantitatively aggregated surge-mortality associations.

DATA SYNTHESIS

Of 17,831 citations, we included 39 studies, 17 of which specifically described surge effects in ICU settings. The majority of studies were from high-income countries (n = 35 studies) and included patients with COVID-19 (n = 31). There were 37 different surge metrics which were mapped into four broad themes, incorporating caseloads either directly as unadjusted counts (n = 11), nested in occupancy (n = 14), including additional factors (e.g., resource needs, speed of occupancy; n = 10), or using indirect proxies (e.g., altered staffing ratios, alternative care settings; n = 4). Notwithstanding metric heterogeneity, 32 of 39 studies (82%) reported detrimental adjusted odds/hazard ratio for caseload surge-mortality outcomes, reporting point estimates of up to four-fold increased risk of mortality. This signal persisted among study subgroups categorized by publication year, patient types, clinical settings, and country income status.

CONCLUSIONS

Pandemic caseload surge was associated with lower survival across most studies regardless of jurisdiction, timing, and population. Markedly variable surge strain measures precluded meta-analysis and findings have uncertain generalizability to lower-middle-income countries (LMICs). These findings underscore the need for establishing a consensus surge metric that is sensitive to capturing harms in everyday fluctuations and future pandemics and is scalable to LMICs.

Trends in Patient Transfers From Overall and Caseload-Strained US Hospitals During the COVID-19 Pandemic

Importance

Transferring patients to other hospitals because of inpatient saturation or need for higher levels of care was often challenging during the early waves of the COVID-19 pandemic. Understanding how transfer patterns evolved over time and amid hospital overcrowding could inform future care delivery and load balancing efforts.

Objective

To evaluate trends in outgoing transfers at overall and caseload-strained hospitals during the COVID-19 pandemic vs prepandemic times.

Design, Setting, and Participants

This retrospective cohort study used data for adult patients at continuously reporting US hospitals in the PINC-AI Healthcare Database. Data analysis was performed from February to July 2023.

Exposures

Pandemic wave, defined as wave 1 (March 1, 2020, to May 31, 2020), wave 2 (June 1, 2020, to September 30, 2020), wave 3 (October 1, 2020, to June 19, 2021), Delta (June 20, 2021, to December 18, 2021), and Omicron (December 19, 2021, to February 28, 2022).

Main Outcomes and Measures

Weekly trends in cumulative mean daily acute care transfers from all hospitals were assessed by COVID-19 status, hospital urbanicity, and census index (calculated as daily inpatient census divided by nominal bed capacity). At each hospital, the mean difference in transfer counts was calculated using pairwise comparisons of pandemic (vs prepandemic) weeks in the same census index decile and averaged across decile hospitals in each wave. For top decile (ie, high-surge) hospitals, fold changes (and 95% CI) in transfers were adjusted for hospital-level factors and seasonality.

Results

At 681 hospitals (205 rural [30.1%] and 476 urban [69.9%]; 360 [52.9%] small with <200 beds and 321 [47.1%] large with ≥200 beds), the mean (SD) weekly outgoing transfers per hospital remained lower than the prepandemic mean of 12.1 (10.4) transfers per week for most of the pandemic, ranging from 8.5 (8.3) transfers per week during wave 1 to 11.9 (10.7) transfers per week during the Delta wave. Despite more COVID-19 transfers, overall transfers at study hospitals cumulatively decreased during each high national surge period. At 99 high-surge hospitals, compared with a prepandemic baseline, outgoing acute care transfers decreased in wave 1 (fold change -15.0%; 95% CI, -22.3% to -7.0%; P < .001), returned to baseline during wave 2 (2.2%; 95% CI, -4.3% to 9.2%; P = .52), and displayed a sustained increase in subsequent waves: 19.8% (95% CI, 14.3% to 25.4%; P < .001) in wave 3, 19.2% (95% CI, 13.4% to 25.4%; P < .001) in the Delta wave, and 15.4% (95% CI, 7.8% to 23.5%; P < .001) in the Omicron wave. Observed increases were predominantly limited to small urban hospitals, where transfers peaked (48.0%; 95% CI, 36.3% to 60.8%; P < .001) in wave 3, whereas large urban and small rural hospitals displayed little to no increases in transfers from baseline throughout the pandemic.

Conclusions and Relevance

Throughout the COVID-19 pandemic, study hospitals reported paradoxical decreases in overall patient transfers during each high-surge period. Caseload-strained rural (vs urban) hospitals with fewer than 200 beds were unable to proportionally increase transfers. Prevailing vulnerabilities in flexing transfer capabilities for care or capacity reasons warrant urgent attention.

Mental health-related structural stigma and discrimination in health and social policies in Nepal: A scoping review and synthesis

AIMS

National policies can be used to reveal structural stigma and discrimination in relation to mental health. This review assesses how structural stigma and discrimination are manifested in the policies and legislations of Government of Nepal.

METHODS

Scoping review methodology was followed to review policy documents (acts of parliament, legislation, policies, strategies, guidelines and official directives) drafted or amended after 2010.

RESULTS

Eighty-nine policies were identified related to health, social welfare, development and regulations which were relevant to people with psychosocial and mental disabilities or have addressed the mental health agendas. Several critical policy failings and gaps are revealed, such as the use of stigmatizing language (e.g., 'insane' or 'lunatic'), inconsistencies within and between policies, deviation from international protocols defining legal capacity and consent, lack of inclusion of the mental health agenda in larger development policies and lack of cost-effective interventions and identification of financing mechanisms. Provisions for people living with mental health conditions included adequate standard of living; attaining standard mental health; the right to exercise legal capacity, liberty and security; freedom from torture or discrimination; and right to live independently. However, other policies contradicted these rights, such as prohibiting marriage, candidacy for and retention of positions of authority and vulnerability to imprisonment.

CONCLUSION

Mental health-related structural stigma and discrimination in Nepal can be identified through the use of discriminator language and provisions in the policies. The structural stigma and discrimination may be addressed through revision of the discriminating policies, integrating the mental health agenda into larger national and provincial policies, and streamlining policies to comply with national and international protocols.

Genomic evaluation of late-term abortion in cows recorded through Dairy Herd Improvement test plans

Late-term abortions cause significant economic loss and are of great concern for dairy herds. Late-term abortions >152 d and <251 d of gestation that terminate a lactation or initiate a new lactation have long been recorded by Dairy Herd Improvement (DHI). For 24.8 million DHI lactations, the average recorded incidence of late-term abortions across all years (2001-2018) was 1.2%. However, the 1.3% incidence of abortions reported in 2012 has declined to <1.0% incidence since 2015. Small adjustments were applied to the 82 million daughter pregnancy rate (DPR), 29 million cow conception rate (CCR), and 9 million heifer conception rate (HCR) records to account for late-term abortions more accurately. Fertility credits for CCR and HCR were changed to treat the last breeding as a failure instead of success if the next calving was coded as a late-term abortion. Similarly, when computing DPR, days open is now set to the maximum value of 250 instead of the reported days open if the next reported calving is an abortion. The test of these changes showed very small changes in standard deviation and high correlations (0.997) of adjusted predicted transmitting abilities (PTA) with official PTA from about 20,000 Holstein bulls born since 2000 with >50% reliability. For late-term abortion as a trait, estimated heritability was only 0.001 and PTA had a standard deviation of only 0.1% for recent sires with high reliability (>75%). Young animal genomic PTA have near 50% reliability but range only from -0.5 to +0.4 because of the low incidence and heritability. Genetic trend was slightly favorable and late-term abortion PTA were correlated favorably by 0.27 with net merit, 0.49 with productive life, 0.33 with livability, 0.23 with CCR, 0.20 with HCR, 0.26 with DPR, -0.31 with somatic cell score, -0.24 with daughter stillbirth, and -0.26 with daughter dystocia. Thus, PTA for late-term abortions should not be needed as a separate fertility trait and instead these minor edit changes should suffice. The PTA for late-term abortions would add little value because national evaluations for current fertility traits already account for those economic losses.

Genomic evaluation of dairy heifer livability

Differences in breeds and sire lines suggest the presence of a genetic component for heifer livability (HLIV). Genomic evaluation for this trait can increase profitability and improve animal health and welfare. Evaluations for HLIV were examined from 3,362,499 calf data records from heifers of all breeds born from 2009 to 2016. Data were obtained from the national cooperator database maintained by the Council on Dairy Cattle Breeding (https://www.uscdcb.com/). The total number of deaths reported was 134,753 (4.01%), which included herds with death loss between 1.5 and 25.5%. Age at death was evaluated and ranged from >2 d of age until the heifer left the herd, with a maximum of 18 mo of age. Records were not included until 3 yr after the birthdate so that live status of contemporaries could be confirmed by a calving date for those animals. Deaths observed until 2 d after birth were considered to be a stillbirth rather than a failure of HLIV. The scale used for analysis of HLIV was 0 (died) or 100 (live), and the heritability estimate was 0.7% based on sire model with restricted maximum likelihood estimation. Genomic predicted transmitting abilities for Holstein ranged from -1.6% to +1.6% with a standard deviation of 0.5%, and genomic predicted transmitting abilities for Jersey ranged from -0.5% to +0.5% with a standard deviation of 0.2%. The mean overall death loss was about 4%. Reliabilities of genomic predictions for young animals averaged 46% for Holsteins and 30% for Jerseys, and corresponding traditional parent average reliabilities averaged 16% and 12%, respectively. Correlations of HLIV were 0.44 with productive life, 0.18 to 0.22 with yield traits, and 0.29 with early first calving on proven Holstein bulls. The HLIV trait had a favorable genetic trend in recent years, likely because of the indirect selection associated with the correlated traits. The trait HLIV should receive 1% of emphasis on the Lifetime Net Merit index, resulting in economic progress worth $50,000/yr. By encouraging more comprehensive recording on calf mortality, the reliabilities of genetic predictions could increase significantly.

Crown Lengthening Surgery for Enhancing Restorative Treatment in Esthetic Zone

For obtaining adequate retention for restoring cases like subgingival caries or extensive caries that shortens the tooth, short clinical crown, and fractures, it is usually necessary to disclose more tooth structure. Crown lengthening procedure is done to increase the clinical crown length for restorative or esthetic reasons without breaching the biologic width. These procedures are also utilized to improve the appearance and retention of restorations placed within the esthetic zone. We report a case of crown lengthening surgery with an internal bevel gingivectomy which was done in our department without compromising tooth support and esthetics.

Metformin use and respiratory outcomes in asthma-COPD overlap

Background

Metformin is associated with improved respiratory outcomes in asthma; however, metformin in COPD and asthma-COPD overlap (ACO) remains unexplored.

Objective

To determine the association between metformin use and respiratory outcomes in COPD and ACO.

Study design and methods

Participants with COPD (FEV1/FVC < 0.70) in the Genetic Epidemiology of COPD study (COPDGene®) were categorized as ACO (n = 510), defined as concurrent physician-diagnosed asthma before age 40 years, or COPD alone (n = 3459). We estimated the association of baseline metformin use with (1) rate of total and severe respiratory exacerbations during follow-up, (2) cross-sectional St. George’s Respiratory Questionnaire (SGRQ) score, six-minute walk distance (6MWD), and post-bronchodilator FEV1 percent predicted (FEV1pp), and (3) 5-year change in SGRQ, 6MWD, and FEV1pp. We also examined change in SGRQ, 6MWD and FEV1pp among participants who initiated metformin during follow-up (n = 108) compared to persistent metformin non-users (n = 2080). Analyses were adjusted for sociodemographic factors, medications, and comorbidities.

Results

Among participants with ACO, metformin use was associated with lower rate of total (adjusted incidence rate ratio [aIRR] 0.3; 95% confidence interval [95%CI] 0.11, 0.77) and severe exacerbations (aIRR 0.29; 95%CI 0.10, 0.89). Among participants with COPD alone, there was no association between metformin use with total (aIRR 0.98; 95%CI 0.62, 1.5) or severe exacerbations (aIRR 1.3; 95% CI 0.68, 2.4) (p-interaction < 0.05). Metformin use was associated with lower baseline SGRQ score (adjusted mean difference [aMD] − 2.7; 95%CI − 5.3, − 0.2) overall. Metformin initiation was associated with improved SGRQ score (aMD –10.0; 95% CI − 18.7, − 1.2) among participants with ACO but not COPD alone (p-interaction < 0.05). There was no association between metformin use and 6MWD or FEV1pp in any comparison.

Conclusions

Metformin use was associated with fewer respiratory exacerbations and improved quality of life among individuals with ACO but not COPD alone. Results suggest a potential role for metformin in ACO which requires further prospective study.

Trial Registry: NCT00608764

Necrotizing Stomatitis in Varicella Zoster Infection

Necrotizing periodontal disease are acute periodontal conditions which can present with simple gingivitis to more complex life threatening condition where it can perforate the skin of cheek. They are found in patients with severe illness, stress and reduced immunity. The prevalence of this whole group of disease is usually very low and is stated frequently as the first manifestation in HIV infection. Herpes zoster, a common dermatological condition is a secondary infection due to re-activation of Varicella zoster virus in a person previously acquiring a chicken pox in his/her lifetime. There are limited scientific literatures citing the occurrence of necrotizing stomatitis in varicella zoster infection. Thus, here we present a detail about a case and management of 46 years old female who had a hospital stay of over 5 days for treatment of Herpes zoster infection of mandibular nerve presented with necrotizing stomatitis lesion within oral cavity.

Lung Function, Coronary Artery Disease, and Mortality in HIV

Rationale: Impaired lung function is a potent independent predictor of coronary artery disease (CAD) in individuals without human immunodeficiency virus (HIV) infection; however, the relationship between lung function and CAD in HIV remains undefined. Objectives: To examine the relationship between lung function, CAD, mortality, and circulating biomarkers in HIV. Methods: Spirometry, diffusing capacity of the lung for carbon monoxide (DlCO), emphysema, coronary artery calcium, mortality, cause of death, and biomarkers were examined in HIV-infected and uninfected individuals enrolled in a cohort study at the University of Pittsburgh. Results were then validated in the Multicenter AIDS Cohort Study (MACS) cohort. Results: We examined data on 234 participants in the Pittsburgh cohort. The mean ± standard deviation age was 49.5 ± 10.2 years old, 82.1% were male, and 67.5% were ever smokers. Among the 177 of 234 individuals with HIV infection, lower DlCO (not forced expiratory volume in 1 second or emphysema) was independently associated with greater coronary artery calcium (odds ratio, 1.43 per 10% lower DlCO; 95% confidence interval, 1.14-1.81). HIV-infected individuals with both reduced DlCO and coronary artery calcium had a much higher mortality than those with either low DlCO or coronary calcium alone or with neither condition. Endothelin-1, a circulating biomarker of endothelial dysfunction, was associated with both lower DlCO and greater coronary artery calcium in those with HIV infection. Results were reproducible in 144 individuals enrolled in the MACS cohort; intercellular adhesion molecule 1 was the biomarker of endothelial dysfunction assessed in the MACS cohort. Conclusions: Impaired DlCO and CAD were associated with each other and with higher mortality in individuals with HIV infection.

Gene set enrichment analysis of SNP data in dairy and beef cattle with bovine respiratory disease

Bovine respiratory disease (BRD) is a complex disease that is associated with infection by bacterial and viral pathogens when cattle fail to adequately respond to stress. The objective of this study was to use gene set enrichment analysis of SNP data (GSEA-SNP) and a network analysis (ingenuity pathway analysis) to identify gene sets, genes within gene sets (leading-edge genes) and upstream regulators associated with BRD in pre-weaned dairy calves and beef feedlot cattle. BRD cases and controls were diagnosed using the McGuirk health scoring system. Holstein calves were sampled from commercial calf-raising facilities in California (1003 cases and 1011 controls) and New Mexico (376 cases and 372 controls). Commercial feedlot cattle were sampled from Colorado (500 cases and 499 controls) and Washington (504 cases and 497 controls). There were 102 and 237 unique leading-edge genes identified in the dairy calf and beef cattle populations respectively. Six leading-edge genes (ADIPOQ, HTR2A, MIF, PDE6G, PRDX3 and SNCA) were associated with BRD in both dairy and beef cattle. Network analysis identified glucose as the most influential upstream regulator in dairy cattle, whereas in beef cattle, TNF was the most influential upstream regulator. The genes, gene sets and upstream regulators associated with BRD have common functions associated with immunity, inflammation and pulmonary disease and provide insights into the mechanisms that are critical to BRD susceptibility in cattle.

Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal

Adaptive evolution in humans has rarely been characterized for its whole set of components, i.e. selective pressure, adaptive phenotype, beneficial alleles and realized fitness differential. We combined approaches for detecting polygenic adaptations and for mapping the genetic bases of physiological and fertility phenotypes in approximately 1000 indigenous ethnically Tibetan women from Nepal, adapted to high altitude. The results of genome-wide association analyses and tests for polygenic adaptations showed evidence of positive selection for alleles associated with more pregnancies and live births and evidence of negative selection for those associated with higher offspring mortality. Lower hemoglobin level did not show clear evidence for polygenic adaptation, despite its strong association with an EPAS1 haplotype carrying selective sweep signals.

Rapid Communication: Subclinical bovine respiratory disease - loci and pathogens associated with lung lesions in feedlot cattle

Bovine respiratory disease (BRD) is an economically important disease of feedlot cattle that is caused by viral and bacterial pathogen members of the BRD complex. Many cases of subclinical BRD go untreated and are not detected until slaughter, when lung lesions are identified. The objectives of this study were to identify which BRD pathogens were associated with the presence of lung lesions at harvest and to identify genomic loci that were associated with susceptibility to lung lesions as defined by consolidation of the lung and/or the presence of fibrin tissue. Steers from a Colorado feedlot (n = 920) were tested for the presence of viral and bacterial pathogens using deep pharyngeal and mid-nasal swabs collected on entry into the study. Pathogen profiles were compared between cattle with or without lung consolidation (LC), fibrin tissue in the lung (FT), a combination of LC and FT in the same lung (lung lesions [LL]), and hyperinflated lungs (HIF) at harvest. Genotyping was conducted using the Illumina BovineHD BeadChip. Genomewide association analyses (GWAA) were conducted using EMMAX (efficient mixed-model association eXpedited), and pseudoheritabilities were estimated. The pathogen profile comparisons revealed that LC (P = 0.01, odds ratio [OR] = 3.37) and LL cattle (P = 0.04, OR = 4.58) were more likely to be infected with bovine herpes virus-1 and that HIF cattle were more likely to be infected with Mycoplasma spp. (P = 0.04, OR = 4.33). Pseudoheritability estimates were 0.25 for LC, 0.00 for FT, 0.28 for LL, and 0.13 for HIF. Because pseudoheritability for FT was estimated to be 0, GWAA results for FT were not reported. There were 4 QTL that were moderately associated (P < 1 × 10⁻⁵) with only LC, 2 that were associated with only LL, and 1 that was associated with LC and LL. Loci associated with HIF included 12 that were moderately associated and 3 that were strongly associated (uncorrected P < 5 × 10−7). A 24-kb region surrounding significant lead SNP was investigated to identify positional candidate genes. Many positional candidate genes underlying or flanking the detected QTL have been associated with signal transduction, cell adhesion, or gap junctions, which have functional relevance to the maintenance of lung health. The identification of pathogens and QTL associated with the presence of lung abnormalities in cattle exhibiting subclinical BRD allows the identification of loci that may not be detected through manifestation of clinical disease alone.

Identification of genes associated with susceptibility to Mycobacterium avium ssp. paratuberculosis (Map) tissue infection in Holstein cattle using gene set enrichment analysis-SNP

Multiple genome-wide association analyses have investigated susceptibility to bovine paratuberculosis, but few loci have been identified across independent cattle populations. A SNP-based gene set enrichment analysis (GSEA-SNP) allows expanded identification of genes with moderate effects on a trait through the enrichment of gene sets instead of identifying only few loci with large effects. Therefore, the objective of this study was to identify genes that were moderately associated with Mycobacterium avium ssp. paratuberculosis (Map) tissue infection using GSEA-SNP in Holstein cattle from the Pacific Northwest (PNW; n = 205) and from the PNW and Northeast (PNW+NE; n = 245) which were previously genotyped with the Illumina BovineSNP50 BeadChip. The GSEA-SNP utilized 4389 gene sets from five databases. For each annotated gene in the UMD3.1 assembly (n = 19,723), the most significant SNP within each gene and its surrounding region (10 kb up- and downstream) was selected as a proxy for that gene. Any gene set with a normalized enrichment score > 2.5 was considered enriched. Thirteen gene sets (8 PNW GSEA-SNP; 5 PNW+NE) were enriched in these analyses and all have functions that relate to nuclear factor kappa beta. Nuclear factor kappa beta is critical to gut immune responses, implicated in host immune responses to other mycobacterial diseases, and has established roles in inflammation as well as cancer. Gene sets and genes moderately associated with Map infection could be used in genomic selection to allow producers to select for less susceptible cattle, lower the prevalence of the disease, and reduce economic losses.

Correction: A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau

[This corrects the article DOI: 10.1371/journal.pone.0175885.].

Antioxidant defense and oxidative damage vary widely among high-altitude residents

OBJECTIVES

People living at high altitude experience unavoidable low oxygen levels (hypoxia). While acute hypoxia causes an increase in oxidative stress and damage despite higher antioxidant activity, the consequences of chronic hypoxia are poorly understood. The aim of the present study is to assess antioxidant activity and oxidative damage in high-altitude natives and upward migrants.

METHODS

Individuals from two indigenous high-altitude populations (Amhara, n = 39), (Sherpa, n = 34), one multigenerational high-altitude population (Oromo, n = 42), one upward migrant population (Nepali, n = 12), and two low-altitude reference populations (Amhara, n = 29; Oromo, n = 18) provided plasma for measurement of superoxide dismutase (SOD) activity as a marker of antioxidant capacity, and urine for measurement of 8-hydroxy-2'-deoxyguanosine (8-OHdG) as a marker of DNA oxidative damage.

RESULTS

High-altitude Amhara and Sherpa had the highest SOD activity, while highland Oromo and Nepalis had the lowest among high-altitude populations. High-altitude Amhara had the lowest DNA damage, Sherpa intermediate levels, and high-altitude Oromo had the highest.

CONCLUSIONS

High-altitude residence alone does not associate with high antioxidant defenses; residence length appears to be influential. The single-generation upward migrant sample had the lowest defense and nearly the highest DNA damage. The two high-altitude resident samples with millennia of residence had higher defenses than the two with multiple or single generations of residence.

A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau

Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their demography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with worldwide genetic variation data. We found a clear signal of genetic stratification across the east-west axis within Tibetan samples. Samples from more eastern locations tend to have higher genetic affinity with lowland East Asians, which can be explained by more gene flow from lowland East Asia onto the plateau. Our findings corroborate a previous report of admixture signals in Tibetans, which were based on a subset of the samples analyzed here, but add evidence for isolation by distance in a broader geospatial context.

High-Altitude Pulmonary Vascular Diseases

More than 140 million people permanently reside in high-altitude regions of Asia, South America, North America, and Africa. Another 40 million people travel to these places annually for occupational and recreational reasons, and are thus exposed to the low ambient partial pressure of oxygen. This review will focus on the pulmonary circulatory responses to acute and chronic high-altitude hypoxia, and the various expressions of maladaptation and disease arising from acute pulmonary vasoconstriction and subsequent remodeling of the vasculature when the hypoxic exposure continues. These unique conditions include high-altitude pulmonary edema, high-altitude pulmonary hypertension, subacute mountain sickness, and chronic mountain sickness.

Magnetotransport of single crystalline NbAs

We report transport measurement in zero and applied magnetic field on a single crystal of NbAs. Transverse and longitudinal magnetoresistance in the plane of this tetragonal structure does not saturate up to 9 T. In the transverse configuration (H ∥ c, I ⊥ c) it is 230,000% at 2 K. The Hall coefficient changes sign from hole-like at room temperature to electron-like below ∼150 K. The electron carrier density and mobility calculated at 2 K based on a single band approximation are 1.8 × 10(19) cm(-3) and 3.5 × 10(5) cm(2) Vs(-1), respectively. These values are similar to reported values for TaAs and NbP, and further emphasize that this class of noncentrosymmetric, transition-metal monopnictides is a promising family to explore the properties of Weyl semimetals and the consequences of their novel electronic structure.

Sustained use of biogas fuel and blood pressure among women in rural Nepal

BACKGROUND

More than two fifths of the world's population cook with solid fuels and are exposed to household air pollution (HAP). As of now, no studies have assessed whether switching to alternative fuels like biogas could impact cardiovascular health among cooks previously exposed to solid fuel use.

METHODS

We conducted a propensity score matched cross-sectional study to explore if the sustained use of biogas fuel for at least ten years impacts blood pressure among adult female cooks of rural Nepal. We recruited one primary cook ≥ 30 years of age from each biogas (219 cooks) and firewood (300 cooks) using household and measured their systolic (SBP) and diastolic blood pressure (DBP). Household characteristics, kitchen ventilation and 24-h kitchen carbon monoxide were assessed. We matched cooks by age, body mass index and socio-economic status score using propensity scores and investigated the effect of biogas use through multivariate regression models in two age groups, 30-50 years and >50 years to account for any post-menopausal changes.

RESULTS

We found substantially reduced 24-h kitchen carbon monoxide levels among biogas-using households. After matching and adjustment for smoking, kitchen characteristics, ventilation status and additional fuel use, the use of biogas was associated with 9.8 mmHg lower SBP [95% confidence interval (CI), -20.4 to 0.8] and 6.5 mmHg lower DBP (95% CI, -12.2 to -0.8) compared to firewood users among women >50 years of age. In this age group, biogas use was also associated with 68% reduced odds [Odds ratio 0.32 (95% CI, 0.14 to 0.71)] of developing hypertension. These effects, however, were not identified in younger women aged 30-50 years.

CONCLUSIONS

Sustained use of biogas for cooking may protect against cardiovascular disease by lowering the risk of high blood pressure, especially DBP, among older female cooks. These findings need to be confirmed in longitudinal or experimental studies.

Quality of life among people living with acquired immune deficiency syndrome receiving anti-retroviral therapy: a study from Nepal

Purpose

The present study was undertaken to determine the impact of acquired immune deficiency syndrome (AIDS) on the quality of life of affected individuals in Nepal.

Patients and methods

A cross sectional study was done among 70 individuals attending the Anti-Retroviral Therapy clinic of the University Hospital in Nepal. Quality of life (QOL) was evaluated using World Health Organization Quality of life questionnaire (WHO QOL-BREF) instrument. Statistical analysis was done using SPSS Version 17.0.

Results

The median scores with interquartile range (IQR) in four domains of QOL in descending order were physical (61; IQR 22), social (58; IQR 33), environmental (56; IQR 13), and psychological (54; IQR 8). Older age was associated with lower perceived overall QOL. Females were more likely to have lower QOL scores in the social and psychological domains. Higher CD4 counts and a married status were significant predictors of higher QOL scores in the environmental domain.

Conclusion

Being older, female, single, and having advanced clinical stage is associated with lower QOL scores in people living with AIDS. Lowest QOL scores were seen in the psychological domain suggesting the need of psychological interventions.

Perception of security by health workforce at workplace in Nepal

BACKGROUND

In Nepal, the relationship of health worker and patient or community people is now deteriorating and the security and safety of health worker is becoming emerging issues. The poor relationship between community people and health worker is hampering the health service especially in rural setting. This study was aimed at finding the security perception and situation of health workforce in Nepal.

METHODS

A cross-sectional descriptive study was conducted using both quantitative and qualitative methods. Out of 404 sample health institutions, 747 health workforce from 375 health institutions were interviewed (<10% non-response rate) using the probability proportionate to size method as per World Health Organization (WHO) guidelines.

RESULTS

Nearly 168 (23%) of health workers felt some level of insecurity at their workplace. Mostly, doctors felt insecure at their workplace 24 (30%) and argued with service users , 26 (32.50%). Feeling of security was highest in central region 160 (83.30%). Nationwide, 121 (16%) of health workers faced some level of arguments with service users, which was highest in Tarai 64 (18.08%). Of the total harassment, both gender based and sexual harassment was higher among female health workers [20 (62.5%) and 13 (56.5%) respectively]. Only, 230 (30.7%) of health workers who suffered from workplace accidents got compensation and treatment.

CONCLUSIONS

Higher proportions of health workers feel insecurity at workplace whereas provision of compensation was minimal. There is a need of strict implementation of Security of the Health Workers and Health Organizations Act, 2066 (2009) for effective health service delivery.

Cardiovascular health risk behavior among medical students in a teaching hospital

BACKGROUND

Medical students are the health care providers of tomorrow. The health behaviors that are acquired in early life and in medical school will influence their future acceptance and practice of preventive strategies including their interaction with patients. The main objective of our study was to assess the health behavior and perceptions of medical students in relation to cardiovascular diseases.

METHODS

A cross sectional descriptive study was done among 159 medical students of Institute of Medicine, Tribhuvan University Teaching Hospital in Kathmandu, Nepal from September 2010 to December 2010. Data collection was done using a self administered questionnaire.

RESULTS

The mean age was 22.9±2.5 yrs and a male:female ratio of 2.1:1. Thirty Five (22%) were current smokers, 56 (35%) indulged in episodic heavy drinking, 25 (15.7%) were overweight, 34 (21%) engaged in recommended amount of physical activitiy,58 (33%) regulated fat consumption and 46 (28%) regulated salt consumption. Regarding developing cardiovascular disease in the future, 85(53%) showed concern but only 33 (38%) of these adopted preventive practices. 101 (64%) believed that their medical school life had a harmful effect on their health.

CONCLUSIONS

Our study shows a high prevalence of cardiovascular risk behaviours among the medical students. This highlights the urgency that we must take to promote preventive knowledge and practices among medical students. This will help them to become prevention oriented clinicians in future to counter the increasing burden of cardiovascular diseases in this part of the world.

Electronic structure of optimally doped pnictide Ba0.6K0.4Fe2As2: a comprehensive angle-resolved photoemission spectroscopy investigation

The electronic structure of the Fe-based superconductor Ba(0.6)K(0.4)Fe(2)As(2) is studied by means of angle-resolved photoemission. We identify dispersive bands crossing the Fermi level forming hole-like (electron-like) Fermi surfaces (FSs) around Γ (M) with nearly nested FS pockets connected by the antiferromagnetic wavevector. Compared to band structure calculation findings, the overall bandwidth is reduced by a factor of 2 and the low energy dispersions display even stronger mass renormalization. Using an effective tight banding model, we fitted the band structure and the FSs to obtain band parameters reliable for theoretical modeling and calculation of physical quantities.

Observation of Dirac cone electronic dispersion in BaFe2As2

We performed an angle-resolved photoemission spectroscopy study of BaFe2As2, which is the parent compound of the so-called 122 phase of the iron-pnictide high-temperature superconductors. We reveal the existence of a Dirac cone in the electronic structure of this material below the spin-density-wave temperature, which is responsible for small spots of high photoemission intensity at the Fermi level. Our analysis suggests that the cone is slightly anisotropic and its apex is located very near the Fermi level, leading to tiny Fermi surface pockets. The bands forming the cone show an anisotropic leading edge gap away from the cone that suggests a nodal spin-density-wave description.

Observation of a novel orbital selective Mott transition in Ca(1.8)Sr(0.2)RuO(4)

We observed a novel orbital selective Mott transition in Ca(1.8)Sr(0.2)RuO(4) by angle-resolved photoemission. While two sets of dispersing bands and the Fermi surface associated with the doubly degenerate d(yz) and d(zx) orbitals are identified, the Fermi surface associated with the wider d(xy) band is missing as a consequence of selective Mott localization. Our theoretical calculations demonstrate that this orbital selective Mott transition is mainly driven by the combined effects of interorbital carrier transfer, superlattice potential, and orbital degeneracy, whereas the bandwidth difference plays a less important role.

Coexistence of competing orders with two energy gaps in real and momentum space in the high temperature superconductor Bi_{2}Sr_{2-x}La_{x}CuO_{6+delta}

Through a combined scanning tunneling microscopy and angle-resolved photoemission spectroscopy study, we report the observation of two distinct gaps (a small and a large gap) that coexist both in real space and in the antinodal region of momentum space, below the superconducting transition temperature (T_{c}) of Bi_{2}Sr_{2-x}La_{x}CuO_{6+delta}. We show that the small gap is associated with superconductivity. The large-gap persists above T_{c}, and seems linked to observed charge ordering. We find a strong correlation between the large and small gaps suggesting that they are affected by similar physical processes.

Competition between antiferromagnetism and superconductivity in the electron-doped cuprates triggered by oxygen reduction

We have performed a systematic angle-resolved photoemission study of as-grown and oxygen-reduced Pr(2-x)CexCuO4 and Pr(1-x)LaCexCuO4 electron-doped cuprates. In contrast with the common belief, neither the band filling nor the band parameters are significantly affected by the oxygen reduction process. Instead, we show that the main electronic role of the reduction process is to remove an anisotropic leading edge gap around the Fermi surface. While the nodal leading edge gap is induced by long-range antiferomagnetic order, the origin of the antinodal one remains unclear.