bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapamycin modulates pulmonary pathology in a murine model of Mycobacterium tuberculosis infection
Authors: Bhatt Kamlesh , Bhagavathula Madhuri , Verma Sheetal , Timmins Graham S. , Deretic Vojo P. , Ellner Jerrold J. , Salgame Padmini 
Published: September 2021

ABSTRACT
Tuberculosis (TB) treatment regimens are lengthy, causing non-adherence to treatment. Inadequate treatment can lead to relapse and the development of drug resistance TB. Furthermore, patients often exhibit residual lung damage even after cure, increasing the risk for relapse and development of other chronic respiratory illnesses. Host-directed therapeutics are emerging as an attractive means to augment the success of TB treatment. In this study, we used C3HeB/FeJ mice as an experimental model to investigate the potential role of rapamycin, a mammalian target of rapamycin inhibitor, as an adjunctive therapy candidate during the treatment of Mycobacterium tuberculosis infection with moxifloxacin. We report that administration of rapamycin with or without moxifloxacin reduced infection-induced lung inflammation, and the number and size of caseating necrotic granulomas. Results from this study strengthen the potential use of rapamycin and its analogs as adjunct TB therapy, and importantly underscore the utility of the C3HeB/FeJ mouse model as a preclinical tool for evaluating host-directed therapy candidates for the treatment of TB.
Sequence diversity and evolution of infectious bursal disease virus in Iraq
Authors: Abbas Ali Hadi , AL saegh Haider Abas , ALaraji Furkan Sabbar 
Published: September 2021

Background: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare. Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2 genes were generated and sequenced. Sequences were then compared with other local and global sequences downloaded from GenBank repositories. Sequence alignment and DNA sequence analyses were achieved using MUSCLE, UGENE and MEGAx software. The molecular clock and sequence evolutionary analyses were applied using MEGAx tools. Results: The strain sequenced in this study belongs to a very virulent Infectious Bursal Disease Virus (vvIBDV) as the DNA and phylogenetic analysis of VP1 and VP2 gene sequences showed a mutual clustering with similar sequences belonging to vvIBDV genogroup 3. Analyses of the hyper variable region of VP2 gene (hvVP2) of IBDV isolates from Iraq indicates a presence of sequence diversity. Interestingly, the two vaccine strains Ventri IBDV Plus and ABIC MB71 that showed the highest sequence similarity to the local isolates in the hvVP2 region are not used in vaccination routine against IBDV in Iraq. Conclusion: Sequences of vvIBDV in Iraq are diverse. Remarkably, some of the available vaccine strains show high sequence similarity with local strains in Iraq; however, they are not included in the routine vaccination programs. Analysis of more samples involving more geographical regions is needed to draw a detailed map of antigenic diversity of IBDV in Iraq.
A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes
Authors: Sutton Granger , Fogel Gary B. , Abramson Bradley , Brinkac Lauren , Michael Todd , Liu Enoch S. , Thomas Sterling 
Published: September 2021

Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. Methods: We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. Results: We show that the core regions determined by our method contain all or almost all essential genes. This demonstrates the accuracy of our method as essential genes should be core genes. We show that we outperform previous methods by this measure. We also explain why there are exceptions to this rule for our method. Conclusions: We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.
Vasoactive agents in acute mesenteric ischaemia in critical care. A systematic review
Authors: Brennan Christopher A , Osei-Bonsu Peter , McClenaghan Rachael Eimear , Nassar Ahmed , Forget Patrice , Kaye Callum , Ramsay George 
Published: September 2021

Background: Acute mesenteric ischaemia (AMI) is a surgical emergency which has an associated high mortality. The mainstay of active treatment includes early surgical intervention, with resection of non-viable bowel, and revascularisation of the ischaemic bowel where possible. Due to the physiological insult of AMI however, perioperative care often involves critical care and the use of vasoactive agents to optimise end organ perfusion. A number of these vasoactive agents are currently available with varied mechanism of action and effects on splanchnic blood flow. However, specific guidance on which is the optimal vasoactive drug to use in these settings is limited. This systematic review aimed to evaluate the current evidence comparing vasoactive drugs in AMI. Methods: A systematic search of Ovid Medline, Ovid Embase, Cochrane CENTRAL and the Cochrane Database of Systematic Review was performed on the 5th of November 2020 to identify randomised clinical trials comparing different vasoactive agents in AMI on outcomes including mortality. The search was performed through the Royal College of Surgeons of England (RCSEng) search support library. Results were analysed using the Rayyan platform, and independently screened by four investigators. Results: 614 distinct papers were identified. After screening, there were no randomised clinical trials meeting the inclusion criteria. Conclusions: This review identifies a gap in literature, and therefore recommends an investigation into current practice and clinician preference in relation to vasoactive agents in AMI. Multicentre randomised controlled trials comparing these medications on clinical outcomes will therefore be required to address this question.
Hospital quality monitoring and evaluation system using linked spreadsheets on Microsoft SharePoint
Authors: Kiroro Francis , Twahir Majid , Kiura Daniel , Kamuyu Ann , Wanyoike Ann 
Published: September 2021

Background Establishment of a systematic way of measurement and utilization of indicators for improvement is one of the most challenging issues in monitoring and evaluation of indicators in healthcare settings. In realizing these fundamental challenges, we designed a monitoring and evaluation system incorporating a hospital-wide quality variance report (QVR) system using linked Microsoft Excel® spreadsheets on Microsoft SharePoint®. Methods Indicators were determined at the departmental/unit level in line with the institutional goals, departmental functions, quality expectations, inputs/outputs, clinical priorities, compliance to policies/procedures/protocols/guidelines/pathways as well as in response to gaps in service delivery picked during root cause analyses. The sample design was determined in accordance with the characteristics of the population. Drawing of sample units was done using a simple random sampling technique without replacement or systematic random sampling. The indicator’s monitoring was enhanced visually by allocating colour codes based on performance across the months and quarters. The action plan tab consisted of a platform that aids in documenting corrective actions arising from the performance reviews. Results and discussion The QVR reporting system ensured a standardized format of monitoring throughout the institution with a reduced turnaround time from data collection to analysis. Further, continuity of the monitoring and evaluation (M&E) system was guaranteed even if an individual left the institution. The analysis of the QVR allowed hospital-wide trending on cross-cutting indicators with consequent ease of communication to multiple stakeholders. The automation has saved time and increased accuracy which has enhanced credible engagements during quality meetings. Conclusions Use of this system greatly enhanced quality performance monitoring in the hospital, identification of major bottlenecks that warranted hospital-wide projects or departmental-level projects. The QVR system enhanced the efficiency and accuracy of quality monitoring from data collection through to performance reviews. The QVR structure allows for customized development of an M&E database application software.
Uncertainties of particulate organic carbon concentrations in the mesopelagic zone of the Atlantic ocean
Authors: Strubinger Sandoval Paul , Dall'Olmo Giorgio , Haines Keith , Rasse Rafael , Ross Jelizaveta 
Published: September 2021

Measurements of particulate organic carbon (POC) in the open ocean provide grounds for estimating oceanic carbon budgets and for modelling carbon cycling. The majority of the published POC measurements have been collected at the sea surface. Thus, POC stocks in the upper layer of the water column are relatively well constrained. However, our understanding of the POC distribution and its dynamics in deeper areas is modest due to insufficient in POC measurements. Moreover, the accuracy of published POC estimates is not always quantified, and neither is it fully understood. In this study, we determined the POC concentrations of samples collected in the upper 500 m during an Atlantic Meridional Transect and described a method for quantifying its experimental uncertainties using duplicate measurements. The analysis revealed that the medians of the total experimental uncertainties associated with our POC concentrations in the productive and mesopelagic zones were 2.5(±1.2) mg/m3 and 2.6(±0.6) mg/m3, respectively. In relative terms, these uncertainties corresponded to ~14% and ~ 35% of POC concentrations, respectively. However, despite our best efforts, we could explain only ~ 21% of the total experimental POC uncertainty. The potential sources of this unexplained portion of uncertainty are discussed.
The Persistent Effects of Short-Term Peer Groups on Performance: Evidence from a Natural Experiment in Higher Education
Authors: Thiemann Petra 
Published: September 2021

This paper studies the persistent effects of short-term peer exposure on long-run performance in a college setting. I exploit the random assignment of undergraduates to peer groups during a mandatory orientation week and track the students’ performance over four years (until graduation). Assignment to orientation week groups with high levels of peer ability is associated with lower performance during the first year at college and a higher probability of early dropout. These adverse effects are driven entirely by the exposure of low-ability students to high-ability peers. Beyond the first year, exposure to higher peer ability during the orientation week negatively affects selection into the college’s most popular major (business administration) and final grade point average. Taken together, the findings suggest that the composition of short-term peer groups matters for individual choices and long-run performance outcomes. This paper was accepted by Yan Chen, decision analysis.
The Crowd Classification Problem: Social Dynamics of Binary-Choice Accuracy
Authors: Becker Joshua Aaron , Guilbeault Douglas , Smith Edward Bishop 
Published: September 2021

Decades of research suggest that information exchange in groups and organizations can reliably improve judgment accuracy in tasks such as financial forecasting, market research, and medical decision making. However, we show that improving the accuracy of numeric estimates does not necessarily improve the accuracy of decisions. For binary-choice judgments, also known as classification tasks—for example, yes/no or build/buy decisions—social influence is most likely to grow the majority vote share, regardless of the accuracy of that opinion. As a result, initially, inaccurate groups become increasingly inaccurate after information exchange, even as they signal stronger support. We term this dynamic the “crowd classification problem.” Using both a novel data set and a reanalysis of three previous data sets, we study this process in two types of information exchange: (1) when people share votes only, and (2) when people form and exchange numeric estimates prior to voting. Surprisingly, when people exchange numeric estimates prior to voting, the binary-choice vote can become less accurate, even as the average numeric estimate becomes more accurate. Our findings recommend against voting as a form of decision making when groups are optimizing for accuracy. For those cases where voting is required, we discuss strategies for managing communication to avoid the crowd classification problem. We close with a discussion of how our results contribute to a broader contingency theory of collective intelligence. This paper was accepted by Lamar Pierce, organizations.
Waiting time for hip fracture surgery: hospital variation, causes, and effects on postoperative mortality
Authors: Kjaervik Cato , Gjertsen Jan-Erik , Engeseter Lars B. , Stensland Eva , Dybvik Eva , Soereide Odd 
Published: September 2021

Aims This study aimed to describe preoperative waiting times for surgery in hip fracture patients in Norway, and analyze factors affecting waiting time and potential negative consequences of prolonged waiting time. Methods Overall, 37,708 hip fractures in the Norwegian Hip Fracture Register from January 2014 to December 2018 were linked with data in the Norwegian Patient Registry. Hospitals treating hip fractures were characterized according to their hip fracture care. Waiting time (hours from admission to start of surgery), surgery within regular working hours, and surgery on the day of or on the day after admission, i.e. ‘expedited surgery’ were estimated. Results Mean waiting time was 22.6 hours (SD 20.7); 36,652 patients (97.2%) waited less than three days (< 72 hours), and 27,527 of the patients (73%) were operated within regular working hours (08:00 to 16:00). Expedited surgery was given to 31,675 of patients (84%), and of these, 19,985 (53%) were treated during regular working hours. Patients classified as American Society of Anesthesiologists (ASA) classes 4 and 5 were more likely to have surgery within regular working hours (odds ratio (OR) 1.59; p < 0.001), and less likely to receive expedited surgery than ASA 1 patients (OR 0.29; p < 0.001). Low-volume hospitals treated a larger proportion of patients during regular working hours than high volume hospitals (OR 1.26; p < 0.001). High-volume hospitals had less expedited surgery and significantly longer waiting times than low and intermediate-low volume hospitals. Higher ASA classes and Charlson Comorbidity Index increased waiting time. Patients not receiving expedited surgery had higher 30-day and one-year mortality rates (OR 1.19; p < 0.001) and OR 1.13; p < 0.001), respectively. Conclusion There is inequality in waiting time for hip fracture treatment in Norway. Variations in waiting time from admission to hip fracture surgery depended on both patient and hospital factors. Not receiving expedited surgery was associated with increased 30-day and one-year mortality rates. Cite this article: Bone Jt Open 2021;2(9):710–720.
On-chip dual-band waveguide Bragg filter with identical subnanometer-bandwidth stopbands near 1310 and 1950  nm wavelengths
Authors: Tu Zhengrui , Zhang Jianhao , Alonso-Ramos Carlos , Le Roux Xavier , Vivien Laurent , Cassan Eric 
Published: September 2021

We propose the realization of an on-chip dual identical narrowband Bragg filter at

∼

1310

and

∼

1950

n
m

wavelengths simultaneously based on the silicon-on-insulator (SOI) platform. By taking advantage of subwavelength corrugation behavior at large wavelengths and the difference in the mode areas of the involved modes at the two widely separated wavelengths, undesired diffraction losses are circumvented while achieving Bragg resonances at the two wavelengths simultaneously. A double-corrugation Bragg grating rib waveguide filter is proposed, with two sets of gratings, the inner one close to the rib operating near 1310 nm wavelength, with the outer grating being designed to achieve a transmission dip around 1950 nm. Introducing a proper lateral misalignment to the set of inner grating indents, a dual identical narrowband Bragg filter with

∼

0.47

n
m

3 dB bandwidth at

∼

1310

n
m

and

∼

1950

n
m

is achieved. The proposed design strategy based on the SOI platform relies on a single-etching fabrication process and presents potential applications in situations where equal-bandwidth filtering is needed in on-chip communications and sensing.
Enhancement of squeezing with cascaded and coherent feedback-controlled degenerate optical parametric amplifiers
Authors: Han Yashuai , Zhang Zhao , Zhou Zhengxian , Qu Jun , He Jun , Wang Junmin 
Published: September 2021

The squeezing level of light on atomic resonance produced by a degenerate optical parametric amplifier (DOPA) is now limited by blue or violet pump-light-induced loss, and it is difficult to improve the squeezing by simply reducing the loss of DOPA. In this study, two promising schemes, namely, the cascaded DOPA (C-DOPA) and the coherent feedback-controlled DOPA (CFC-DOPA), are theoretically discussed. For a ideal case, the CFC-DOPA can realize infinite squeezing output but requires almost infinite accuracy in phase locking. For a practical case with feasible physical parameters of realistic systems, the performance of squeezing enhancement for the C-DOPA and CFC-DOPA is compared. The C-DOPA shows advantages in the megahertz frequency range, while the CFC-DOPA shows advantages in the low-frequency range. At a general analysis frequency of 2 MHz, C-DOPA shows better robustness against the loss of the system. As a price, it requires a smaller instability tolerance for phase locking. With the C-DOPA, the squeezing on Rb atomic resonance can be pushed from

−

5

d
B

to

−

7

d
B

. Our analytical results can provide a valuable reference for designing experimental devices to efficiently produce high-quality squeezed light on atomic resonance, which has potential applications in quantum information processing and quantum metrology.
The prevalence and clinical features of pulmonary embolism in patients with AE-COPD: A meta-analysis and systematic review
Authors: Fu Xiaofang , Zhong Yonghong , Xu Wucheng , Ju Jiangang , Yu Min , Ge Minjie , Gu Xiaofei , Chen Qingqing , Sun Yibo , Huang Huaqiong , Shen Linfeng 
Published: September 2021

BackgroundThe prevalence of pulmonary embolism (PE) in the acute exacerbation of chronic obstructive pulmonary disease (AE-COPD) is highly controversial. We conducted a systematic review and meta-analysis to summarize the epidemiology and characteristics of PE with AE-COPD for current studies.MethodsWe searched the PubMed, EMBASE, Cochrane Library and Web of Science databases for studies published prior to October 21, 2020. Pooled proportions with 95% confidence intervals (95% CIs) were calculated using a random effects model. Odds ratios (ORs) and mean differences (MDs) with 95% confidence intervals were used as effect measures for dichotomous and continuous variables, respectively.ResultsA total of 17 studies involving 3170 patients were included. The prevalence of PE and deep vein thrombosis (DVT) in AE-COPD patients was 17.2% (95% CI: 13.4%-21.3%) and 7.1% (95% CI: 3.7%-11.4%%), respectively. Dyspnea (OR = 6.77, 95% CI: 1.97–23.22), pleuritic chest pain (OR = 3.25, 95% CI: 2.06–5.12), lower limb asymmetry or edema (OR = 2.46, 95% CI:1.51–4.00), higher heart rates (MD = 20.51, 95% CI: 4.95–36.08), longer hospital stays (MD = 3.66, 95% CI: 3.01–4.31) were associated with the PE in the AE-COPD patients. Levels of D-dimer (MD = 1.51, 95% CI: 0.80–2.23), WBC counts (MD = 1.42, 95% CI: 0.14–2.70) were significantly higher and levels of PaO2was lower (MD = -17.20, 95% CI: -33.94- -0.45,P<0.05) in the AE-COPD with PE group. The AE-COPD with PE group had increased risk of fatal outcome than the AE-COPD group (OR = 2.23, 95% CI: 1.43–3.50).ConclusionsThe prevalence of PE during AE-COPD varies considerably among the studies. AE-COPD patients with PE experienced an increased risk of death, especially among the ICU patients. Understanding the potential risk factors for PE may help clinicians identify AE-COPD patients at increased risk of PE.Prospero registration numberCRD42021226568.
Risk factors for hospitalization among persons with COVID-19—Colorado
Authors: Vahey Grace M. , McDonald Emily , Marshall Kristen , Martin Stacey W. , Chun Helen , Herlihy Rachel , Tate Jacqueline E. , Kawasaki Breanna , Midgley Claire M. , Alden Nisha , Killerby Marie E. , Staples J. Erin ,   on behalf of the Colorado Investigation Team
Published: September 2021

Background
Most current evidence on risk factors for hospitalization because of coronavirus disease 2019 (COVID-19) comes from studies using data abstracted primarily from electronic health records, limited to specific populations, or that fail to capture over-the-counter medications and adjust for potential confounding factors. Properly understanding risk factors for hospitalization will help improve clinical management and facilitate targeted prevention messaging and forecasting and prioritization of clinical and public health resource needs.

Objectives
To identify risk factors for hospitalization using patient questionnaires and chart abstraction.

Methods
We randomly selected 600 of 1,738 laboratory-confirmed Colorado COVID-19 cases with known hospitalization status and illness onset during March 9–31, 2020. In April 2020, we collected demographics, social history, and medications taken in the 30 days before illness onset via telephone questionnaire and collected underlying medical conditions in patient questionnaires and medical record abstraction.

Results
Overall, 364 patients participated; 128 were hospitalized and 236 were non-hospitalized. In multivariable analysis, chronic hypoxemic respiratory failure with oxygen requirement (adjusted odds ratio [aOR] 14.64; 95% confidence interval [CI] 1.45–147.93), taking opioids (aOR 8.05; CI 1.16–55.77), metabolic syndrome (aOR 5.71; CI 1.18–27.54), obesity (aOR 3.35; CI 1.58–7.09), age ≥65 years (aOR 3.22; CI 1.20–7.97), hypertension (aOR 3.14; CI 1.47–6.71), arrhythmia (aOR 2.95; CI 1.00–8.68), and male sex (aOR 2.65; CI 1.44–4.88), were significantly associated with hospitalization.

Conclusion
We identified patient characteristics, medications, and medical conditions, including some novel ones, associated with hospitalization. These data can be used to inform clinical and public health resource needs.