bluuebunny/crossref_metadata_2025_split huggingface dataset:
Corynebacterium Keratitis: Pure Versus Mixed Infection and Antibiotic Susceptibility Patterns From Different Tertiary Eye Care Centers
Authors: Soni Tanvi , Gunasekaran Rameshkumar , Das Sujata , Mitra Sanchita , Prajna Namperumalsamy Venkatesh , Prajna Lalitha , Sharma Savitri , Mohamed Ashik 
Published: November 2021

Purpose:
The objective of this study was to compare the clinical and microbiological profiles of culture-proven pure Corynebacterium keratitis with mixed infection and their antibiotic susceptibility patterns over a 2-year period.

Methods:
A retrospective analysis of culture-proven cases of Corynebacterium keratitis over a 2-year period was performed in 3 different tertiary eye care centers. All isolates were tested for antibiotic susceptibility in vitro using the disc-diffusion method for 7 antibiotics.

Results:
Altogether 108 cases were identified as culture-positive Corynebacterium keratitis in 3 tertiary eye care centers. Of these, 60.2% (n = 65) and 39.8% (n = 43) of cases were due to pure Corynebacterium and mixed infection, respectively. The mean duration of symptoms was 23.2 ± 29.6 days. In the mixed-infection group, fungus was identified as the coexistent pathogen in 22 cases (51.1%). Ocular surface disorder was the most common risk factor (33.9%) in Corynebacterium keratitis. The most frequently isolated species was Corynebacterium amycolatum (22.2%) in both groups. Therapeutic keratoplasty was performed in 8.3% of cases. There was no significant difference in the outcome between the 2 groups. Cefazolin resistance was seen in 13.9% of patients, and all isolates were susceptible to vancomycin. The resistance pattern showed emerging resistance toward fluoroquinolone because the isolates were resistant to gatifloxacin (58.3%), moxifloxacin (47.2%), ciprofloxacin (54.6%), and ofloxacin (45.4%).

Conclusions:
Ocular surface disorder is the most common risk factor in Corynebacterium keratitis. Although fluoroquinolones are commonly used as first-line therapy in microbial keratitis, the in vitro resistance pattern indicates that these are less likely to be effective in infection with Corynebacterium species.
Transbronchial lung cryobiopsy for the diagnosis of interstitial lung diseases
Authors: Ravaglia Claudia , Poletti Venerino 
Published: November 2021

Purpose of review
Transbronchial lung cryobiopsy has shown promise in several studies in providing meaningful histological information in the multidisciplinary team diagnosis of fibrotic interstitial lung diseases. The purpose of this review is to describe recent literature providing support for the formal integration of cryobiopsy into the algorithm for interstitial lung disease diagnosis.

Recent findings
Histopathological concordance between cryobiopsy and surgical biopsy and diagnostic agreement at multidisciplinary discussion have been reported good; furthermore, cryobiopsy may provide an increased diagnostic confidence to a level likely to influence management. Finally, although cryobiopsy is more likely to provide a probable usual interstitial pneumonia (UIP) pattern than a definite UIP pattern, given the limited sampling of sub-pleural lung parenchyma in most cases, finding of a probable UIP pattern at cryobiopsy samples is strongly predictive of a definite UIP pattern in the corresponding surgical biopsy and when a UIP pattern is found on cryobiopsy sample, this is associated with higher mortality compared with other histological patterns.

Summary
Cryobiopsy is becoming a valid alternative to surgical lung biopsy for making histopathological diagnosis in patients with interstitial lung diseases of undetermined type in experienced centres, with standardized protocols, in order to have the best risks/diagnostic yields ratio.
A Call to Address RN, Social Work, and Advanced Practice Registered Nurses in Nursing Homes
Authors: Popejoy Lori L. , Vogelsmeier Amy A. , Canada Kelli E. , Kist Shari , Miller Steven J. , Galambos Colleen , Alexander Gregory L. , Crecelius Charles , Rantz Marilyn 
Published: November 2021

Background:
US nursing homes (NHs) have struggled to overcome a historic pandemic that laid bare limitations in the number and clinical expertise of NH staff.

Problem:
For nurse staffing, current regulations require only one registered nurse (RN) on duty 8 consecutive hours per day, 7 days per week, and one RN on call when a licensed practical/vocational nurse is on duty. There is no requirement for a degreed or licensed social worker, and advanced practice registered nurses (APRNs) in NHs cannot bill for services.

Approach:
It is time to establish regulation that mandates a 24-hour, 7-day-a-week, on-site RN presence at a minimum requirement of 1 hour per resident-day that is adjusted upward for greater resident acuity and complexity. Skilled social workers are needed to improve the quality of care, and barriers for APRN billing for services in NHs need to be removed.

Conclusions:
Coupling enhanced RN and social work requirements with access to APRNs can support staff and residents in NHs.
Protocol for a mixed methods exploratory study of success factors to escalation of care: the SUFFICE study
Authors: Ede J , Watkinson P , Endacott R 
Published: November 2021

AbstractBackgroundIn the United Kingdom, hospital patients suffer preventable deaths (failure to rescue) and delayed admission to the Intensive Care Unit because of poor illness recognition. This problem has consistently been identified in care reviews. Strategies to improve deteriorating ward patient care, such as early warning systems and specialist care teams (Critical Care Outreach or Rapid Response), have not reliably demonstrated reductions to patient deaths. Current research focuses on failure to rescue, but further reductions to patient deaths are possible, by examining care of unwell hospital patients who are rescued (successfully treated). Our primary objective is to develop a framework of care escalation success factors that can be developed into a complex intervention to reduce patient mortality and unnecessary admissions to the Intensive Care Unit (ICU).Methods and AnalysisSUFFICE is a multicentre mixed-methods, exploratory sequential study examining rescue events in the acutely unwell ward patient in two National Health Service Trusts with Teaching Hospital status. The study will constitute four key phases. Firstly, we will observe ward care escalation events to generate a theoretical understanding of the process of rescue. Secondly, we will review care records from unwell ward patients in whom an ICU admission was avoided to identify care success factors. Thirdly, we will conduct staff interviews with expert doctors, nurses, and Allied Health Professionals to identify how rescue is achieved and further explore care escalation success factors identified in the first two study phases. The final phase involves integrating the study data to generate the theoretical basis for the framework of care escalation success factors.Ethics and DisseminationEthical approval has been obtained through the Queen Square London Research and Ethics committee (REC Ref 20/HRA/3828; CAG-20CAG0106). Study results will be of interest to critical care, nursing and medical professions and results will be disseminated at national and international conferences.Trial Registration NumberISRCTN 38850
Determinants and Magnitude of Neonatal Sepsis at Hiwot Fana Comprehensive Specialized University Hospital, Harar, Ethiopia: A Cross-Sectional Study
Authors: Feleke Astawus Alemayehu , Abdella Mohammed Yusuf , W/Mariam Abebaw Demissie 
Published: November 2021

AbstractIntroductionNeonatal sepsis is a serious blood bacterial infection in neonates at the age of equal to or less than 28 days of life, and it’s still the major significant cause of death and long-term morbidity in developing countries. Therefore, this study has assessed the prevalence and related factors with neonatal sepsis among new born admitted to the neonatal intensive care unit at Hiwot Fana Comprehensive Specialized University Hospital, Harar, Ethiopia.MethodsAn institutional based retrospective cross-sectional study design was conducted among 386 neonates admitted to NICU from September 2017 to August 2019 G.C. A systematic random sampling method was used. Data was analyzed using SPSS V.26. Descriptive summary statistics was done. Bivariate analysis was computed to identify association between dependent and independent variables. Multivariate analysis was used to control possible confounder variables and variables with p-value <0.05 were declared as having statistically significant association.ResultThe prevalence of neonatal sepsis was 53.1% and 59.5% were males. Among the total neonates who had sepsis, 67.8% had early neonatal sepsis. Among neonatal factors, preterm neonates (AOR: 8.1, 95%CI: 2.1, 31.2), birth asphyxia (AOR: 4.7, 95%CI: 1.6, 13.6); and among maternal factors, urban residence (AOR: 0.26, 95%CI: 0.1, 0.5), ANC attendance (AOR: 0.32, 95%CI: 0.2, 0.6), SVD (AOR: 0.047, 95%CI: 0.01, 0.2), Maternal antibiotic use (AOR: 0.39; 95%CI: 0.2, 0.8), duration of rupture of membrane < 12 hours (AOR: 0.11; 95%CI: 0.05, 0.2) were found to have significant association with neonatal sepsis.ConclusionOverall, the magnitude of neonatal sepsis was high. Being preterm, low birth weight and having birth asphyxia were found to significantly increase the odds of neonatal sepsis. Urban residence, having ANC follow up, giving birth by SVD and CS, history of antibiotic use and having rupture of membrane < 18 hours were found to significantly decrease the odds of neonatal sepsis.
Immunogenicity and adverse events of priming with inactivated whole SARS-CoV-2 vaccine (CoronaVac) followed by boosting the ChAdOx1 nCoV-19 vaccine
Authors: Mahasirimongkol Surakameth , Khunphon Athiwat , Kwangsukstid Oraya , Sapsutthipas Sompong , Wichaidit Minkwan , Rojanawiwat Archawin , Wichuckchinda Nuanjun , Puangtubtim Wiroj , Pimpapai Warangluk , Soonthorncharttrawat Sakulrat , Wanitchang Asawin , Jongkaewwattana Anan , Srisutthisamphan Kanjana , Phainupong Daraka , Thawong Penpitcha , Piboonsiri Pundharika , Sawaengdee Warittha , Somporn Thitiporn , Ritthitham Kanokphon , Chumpol Supaporn , Pinyosukhee Nadthanan , Wichajarn Rattanawadee , Dhepaksorn Panadda , Iamsiritahworn Sopon , Phumiamorn Supaporn 
Published: November 2021

AbstractBackgroundResponding to SARS-CoV-2 Delta variants escaped the vaccine-induced immunity and waning immunity from the inactivated whole virus vaccine, Thailand recently proposed a heterologous inactivated whole virus vaccine (CoronaVac) viral vector vaccine (ChAdOx1 nCoV-19) prime-boost vaccine regimen(I/V). This study aims to evaluate the immunogenicity and adverse events of this regimen by comparison with homologous CoronaVac, ChAdOx1 nCoV-19, and convalescent serum.MethodImmunogenicity was evaluated by the level of IgG antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein (S1 subunit) (anti-S RBD). At 2 weeks following the second dosage, a selection of random samples was tested for plaque reduction neutralisation (PRNT) and Pseudotype-Based Microneutralization test (PVNT) against SARS-CoV-2 variants of concern (VOCs). The safety profile of heterologous CoronaVac-ChAdOx1 nCoV-19 prime-boost vaccine regimen was described by interviewing at the 1-month visit.ResultBetween April to August 2021,426 participants were included in the study, with 155 obtaining CoronaVac-ChAdOx1 nCoV-19(I/V),32 obtaining homologous CoronaVac(I/I),47 obtaining homologous ChAdOx1 nCoV-19(V/V),169 with history covid-19 infection. Geometric mean titers (GMTs) of anti-S RBD level in the I/V group compare 2wks and 4 wks (873.9 vs 639,p=0.00114).At 4 wks, GMTs of anti-S RBD level in I/V group was 639, 95% CI 63-726,and natural infection group 177.3, 95% CI 42-221, and V/V group 211.1, 95% CI 77-152, and I/I group 108.2, 95% CI 77-152; all p<0.001).At 2 wks, The GMTs of 50%PRNT of 19 sampling from the I/V group is 434.5, 95% CI 326-579, against wild type and 80.4, 95% CI 56-115, against alpha and 67.4, 95% CI 48-95, against delta and 19.8, 95% CI 14-30, against beta; all p<0.001. At 2 wks, The GMTs of 50%PVNT of 15 sampling from the I/V group is 597.8, 95% CI 368-970, against wild type and 163.9, 95% CI 89-301, against alpha and 157.7, 95% CI 66-378, against delta. The AEs in the I/V schedule were well tolerated and generally unremarkable.ConclusionThe I/V vaccination is a mixed regimen that induced higher immunogenicity and shall be considered for responding to Delta Variants when only inactivated whole virus vaccine and viral vector vaccine was available.
A need of COVID19 vaccination for children aged <12 years: Comparative evidence from the clinical characteristics in patients during a recent Delta surge (B.1.617.2)
Authors: Li Hongru , Lin Haibin , Chen Xiaoping , Li Hang , Li Hong , Lin Sheng , Huang Liping , Chen Gongping , Zheng Guilin , Wang Shibiao , Hu Xiaowei , Huang Handong , Tu Haijian , Li Xiaoqin , Ji Yuejiao , Zhong Wen , li Qing , Fang Jiabin , Lin Qunying , Yu Rongguo , Xie Baosong 
Published: November 2021

AbstractObjectiveTo evaluate the necessity of Covid-19 vaccination in children aged < 12 y by comparing the clinical characteristics in unvaccinated children aged < 12 y with vaccinated patients aged ≥ 12y during the Delta surge (B.1.617.2) in Putian, Fujian, China.MethodsA total of 226 patients with SARS-Cov-2 Delta variant (B.1.167.2; confirmed by Realtime PCR positive and sequencing) were enrolled from Sep 10th to Oct 20th, 2021, including 77 unvaccinated children (aged < 12y) and 149 people aged ≥ 12y, mostly vaccinated. The transmission route was explored and the clinical data of two groups were compared; the effect factors for the time of the nucleic acid negativization (NAN) were examined by R statistical analysis.ResultsThe Delta surge in Putian spread from children in schools to factories, mostly through family contact. Compared with those aged ≥ 12y, patients aged < 12y accounted for 34.07% of the total and showed milder fever, less cough and fatigue; they reported higher peripheral blood lymphocyte counts [1.84(1.32,2.71)×10^9/L vs. 1.31(0.94,1.85)×10^9/L; p<0.05), higher normal CRP rate (92.21% vs. 57.72%), lower IL-6 levels [5.28(3.31,8.13) vs. 9.10(4.37,15.14); p< 0.05]. Upon admission, their COVID19 antibodies (IgM and IgG) and IgG in convalescence were lower [0.13(0.00,0.09) vs. 0.12(0.03,0.41), p<0.05; 0.02(0.00,0.14) vs. 1.94(0.54,6.40), p <0.05; 5.46(2.41,9.26) vs. 73.63 (54.63,86.55), p<0.05, respectively], but longer NAN time (18 days vs. 16 days, p=0.13).ConclusionChildren aged < 12y may be critical hidden spreaders, which indicates an urgent need of vaccination for this particular population.
An economic, square-shaped flat-field illumination module for TIRF-based super-resolution microscopy
Authors: Lam Jeff Y.L. , Wu Yunzhao , Dimou Eleni , Zhang Ziwei , Cheetham Matthew R. , Körbel Markus , Xia Zengjie , Klenerman David , Danial John S.H. 
Published: November 2021

AbstractSuper-resolution (SR) microscopy allows complex biological assemblies to be observed with remarkable resolution. However, the presence of uneven Gaussian-shaped illumination hinders its use in quantitative imaging or high-throughput assays. Methods developed to circumvent this problem are often expensive, hard-to-implement, or not applicable to total internal reflection fluorescence (TIRF) imaging. We herein demonstrate a cost-effective method to overcome these challenges using a small square-core multimodal optical fibre as the coupler. We characterise our method with synthetic, recombinant and cellular systems imaged under TIRF and highly inclined and laminated optical sheet (HILO) illuminations to demonstrate its ability to produce highly uniform images under all conditions.
Bacterial diet modulates tamoxifen-induced death via host fatty acid metabolism
Authors: Diot Cédric , García-González Aurian P. , Vieira Andre F. , Walker Melissa , Honeywell Megan , Doyle Hailey , Ponomarova Olga , Rivera Yomari , Na Huimin , Zhang Hefei , Lee Michael , Olsen Carissa P. , Walhout Albertha J.M. 
Published: November 2021

AbstractTamoxifen is a selective estrogen receptor (ER) modulator that is used to treat ER-positive breast cancer, but that at high doses kills both ER-positive and ER-negative breast cancer cells. We recapitulate this off-target effect inCaenorhabditis elegans, which does not have an ER ortholog. We find that different bacteria dramatically modulate tamoxifen toxicity inC. elegans, with a three-order of magnitude difference between animals fedEscherichia coli,Comamonas aquatica, andBacillus subtilis. Remarkably, host fatty acid (FA) biosynthesis mitigates tamoxifen toxicity, and different bacteria provide the animal with different FAs, resulting in distinct FA profiles. Surprisingly these bacteria modulate tamoxifen toxicity by different death mechanisms, some of which are modulated by FA supplementation and others by antioxidants. Together, this work reveals a complex interplay between microbiota, FA metabolism and tamoxifen toxicity that may provide a blueprint for similar studies in more complex mammals.
Cell cycle stage classification using phase imaging with computational specificity
Authors: He Yuchen R. , He Shenghua , Kandel Mikhail E. , Lee Young Jae , Hu Chenfei , Sobh Nahil , Anastasio Mark A. , Popescu Gabriel 
Published: November 2021

AbstractTraditional methods for cell cycle stage classification rely heavily on fluorescence microscopy to monitor nuclear dynamics. These methods inevitably face the typical phototoxicity and photobleaching limitations of fluorescence imaging. Here, we present a cell cycle detection workflow using the principle of phase imaging with computational specificity (PICS). The proposed method uses neural networks to extract cell cycle-dependent features from quantitative phase imaging (QPI) measurements directly. Our results indicate that this approach attains very good accuracy in classifying live cells into G1, S, and G2/M stages, respectively. We also demonstrate that the proposed method can be applied to study single-cell dynamics within the cell cycle as well as cell population distribution across different stages of the cell cycle. We envision that the proposed method can become a nondestructive tool to analyze cell cycle progression in fields ranging from cell biology to biopharma applications.TeaserWe present a non-destructive, high-throughput method for cell cycle detection combining label-free imaging and deep learning.
Biogeographic multi-species occupancy models for large-scale survey data
Authors: Socolar Jacob B. , Mills Simon C. , Haugaasen Torbjørn , Gilroy James J. , Edwards David P. 
Published: November 2021

AbstractEcologists often seek to infer patterns of species occurrence or community structure from survey data. Hierarchical models, including multi-species occupancy models (MSOMs), can improve inference by pooling information across multiple species via random effects. Originally developed for local-scale survey data, MSOMs are increasingly applied to larger spatial scales that transcend major abiotic gradients and dispersal barriers. At biogeographic scales, the benefits of partial pooling in MSOMs trade off against the difficulty of incorporating sufficiently complex spatial effects to account for biogeographic variation in occupancy across multiple species simultaneously.We show how this challenge can be overcome by incorporating pre-existing range information into MSOMs, yielding a ‘biogeographic multi-species occupancy model’ (bMSOM). We illustrate the bMSOM using two published datasets: Parulid warblers in the United States Breeding Bird Survey, and entire avian communities in forests and pastures of Colombia’s West Andes.Compared to traditional MSOMs, the bMSOM provides dramatically better predictive performance at lower computational cost. The bMSOM avoids severe spatial biases in predictions of the traditional MSOM and provides principled species-specific inference even for never-observed species.Incorporating pre-existing range data enables principled partial pooling of information across species in large-scale MSOMs. Our biogeographic framework for multi-species modeling should be broadly applicable in hierarchical models that predict species occurrences, whether or not false-absences are modeled in an occupancy framework.
Immunogenicity of COVID-19 vaccines in patients with haematological malignancy: A systematic review and meta-analysis
Authors: Teh Joanne S.K. , Coussement Julien , Neoh Zoe C. F. , Spelman Tim , Lazarakis Smaro , Slavin Monica A. , Teh Benjamin W. 
Published: November 2021

AbstractThe objectives of this study were to assess the immunogenicity and safety of COVID-19 vaccines in patients with haematological malignancy. A systematic review and meta-analysis of clinical studies of immune responses to COVID-19 vaccination stratified by underlying malignancy and published from 1 January 2021 to 31 August 2021 was conducted using MEDLINE, EMBASE and CENTRAL. Primary outcome was the rate of seropositivity following 2 doses of COVID-19 vaccine with rates of seropositivity following 1 dose, rates of positive neutralising antibody (nAb), cellular responses and adverse events as secondary outcomes. Rates were pooled from single arm studies while rates of seropositivity were compared against the rate in healthy controls for comparator studies using a random effects model and expressed as a pooled odds ratio with 95% confidence intervals.Forty-four studies (16 mixed group, 28 disease specific) with 7064 patients were included in the analysis (2331 following first dose, 4733 following second dose). Overall seropositivity rates were 61-67% following 2 doses and 37-51% following 1 dose of COVID-19 vaccine. The lowest seropositivity rate was 51% in CLL patients and was highest in patients with acute leukaemia (93%). Following 1 dose, nAb and cellular response rates were 18-63% and 33-86% respectively. Active treatment, ongoing or recent treatment with targeted and CD-20 monoclonal antibody therapies within 12 months was associated with poor COVID-19 vaccine immune responses. New approaches to prevention are urgently required to reduce COVID-19 infection morbidity and mortality in high-risk patient groups that respond poorly to COVID-19 vaccination.
PacRAT: A program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment
Authors: Yeh Chiann-Ling C , Amorosi Clara J , Showman Soyeon , Dunham Maitreya J 
Published: November 2021

AbstractMotivationUse of PacBio sequencing for characterizing barcoded libraries of genetic variants is on the rise. PacBio sequencing is useful in linking variant alleles in a library with their associated barcode tag. However, current approaches in resolving PacBio sequencing artifacts can result in a high number of incorrectly identified or unusable reads.ResultsWe developed a PacBio Read Alignment Tool (PacRAT) that improves the accuracy of barcode-variant mapping through several steps of read alignment and consensus calling. To quantify the performance of our approach, we simulated PacBio reads from eight variant libraries of various lengths and showed that PacRAT improves the accuracy in pairing barcodes and variants across these libraries. Analysis of real (non-simulated) libraries also showed an increase in the number of reads that can be used for downstream analyses when using PacRAT.AvailabilityPacRAT is written in Python and is freely available on GitHub (https://github.com/dunhamlab/PacRAT).