bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robot-assisted artificial urinary sphincter implantation
Authors: Peyronnet Benoit , Gray Gary , Capon Grégoire , Cornu Jean-Nicolas , Van Der Aa Frank 
Published: November 2020

Purpose of review
The aim of the present manuscript was to provide an overview on the current state of robotic artificial urinary sphincter (AUS) implantation in male and female patients.

Recent findings
Over the past few years, several series have been reported, with promising outcomes for the most part. This has contributed to expand the use of bladder neck AUS, especially in female patients, which was, until then, hampered by its perioperative morbidity.

Summary
Robotic AUS has been developed to overcome the technical challenge of bladder neck implantation in female patients and in specific male subgroups, especially self-catheterizing neurological patients. All the series of robotic AUS implantation published in the past few years reported much lower rates of cuff erosion and AUS explantation than the historical open cohorts suggesting that the robotic approach might become the standard for female AUS implantation. This less morbid approach along with technological improvement of the AUS device may contribute to make it a more popular option in the treatment of female stress urinary incontinence due to intrinsic sphincter deficiency. There are much less data available on robotic bladder neck AUS implantation in male patients.
A follow-up study shows no new infections caused by patients with repeat positive of COVID-19 in Wuhan
Authors: Wu Xiaomin , Wang Zengmiao , He Zhenyu , Li Yapin , Wu Yating , Wang Huaiji , Liu Yonghong , Hao Fanghua , Tian Huaiyu 
Published: November 2020

AbstractBackgroundIt has been reported that a few recovered COVID-19 patients could suffer repeat positive, testing positive for the SARS-CoV-2 virus again after they were discharged from hospital. Understanding the epidemiological characteristics of patients with repeat positive is vital in preventing a second wave of COVID-19.MethodsIn this study, the epidemiological and clinical features for 20,280 COVID-19 patients from multiple centers between 31 December 2019 and 4 August 2020 in Wuhan were collected and followed. In addition, the RT-qPCR testing results for 4,079 individuals who had close contact with the patients suffering repeat positive were also obtained.Results2,466 (12.16%) of 20,280 patients presented with a repeat positive of SARS-CoV-2 after they were discharged from hospital. 4,079 individuals had close contact with them. The PCR result were negative for the 4,079 individuals.ConclusionsBy a follow-up study in Wuhan, we show the basic characteristics of patients with repeat positive and no new infections caused by patients with repeat positive of COVID-19.
Are pregnant women satisfied with perinatal standards of care during COVID-19 pandemic?
Authors: Ravaldi Claudia , Mosconi Laura , Crescioli Giada , Ricca Valdo , Vannacci Alfredo 
Published: November 2020

AbstractCOVID-19 restrictive measures severely impacted maternity services worldwide, but little is known about the differences in women’s concerns, perception of the modifications of maternity services and childbirth programs at different times during the pandemic. Here we report data from the first COVID-19 wave in Italy, during the 2020 national lockdown (March-April) and soon after lockdown release (May).1307 pregnant women answered the survey during national lockdown (phase 1) or after restrictive measures were released (phase 2). Women reported a significantly higher COVID-19 concern during phase 1 than during phase 2 (2.34 SD 0.5 vs 2.12 SD 0.5 on a Likert scale 0-3; p<0.001). Several domains of perinatal care were affected during COVID-19 lockdown: while antenatal visits, the use of technology to keep in touch with healthcare professionals, and closeness of caregivers were generally more appreciated (especially during phase 2), women reported the greatest difficulties in receiving clear information on hospitalization, birth plan and partner’s presence at birth.Italian pregnant women’s worries about the effects of the pandemic on health and their perception of quality in the organization of maternity services improved during lockdown, but they continued to represent a challenge in May, especially regarding organizational aspects of hospitalization and childbirth.
Comprehensive genomic profiling of 30,000 consecutive solid tumors
Authors: Tomlins Scott A. , Hovelson Daniel H. , Suga Jennifer M. , Anderson Daniel M. , Koh Han A. , Dees Elizabeth C. , McNulty Brendan , Burkard Mark E. , Guarino Michael , Khatri Jamil , Safa Malek M. , Matrana Marc R. , Yang Eddy S. , Menter Alex R. , Parsons Benjamin M. , Slim Jennifer N. , Thompson Michael A. , Hwang Leon , Edenfield William J. , Nair Suresh , Onitilo Adedayo , Siegel Robert , Miller Alan , Wassenaar Timothy , Irvin William J. , Schulz William , Padmanabhan Arvinda , Harish Vallathucherry , Gonzalez Anneliese , Mansoor Abdul Hai , Kellum Andrew , Harms Paul , Drewery Stephanie , Falkner Jayson , Fischer Andrew , Hipp Jennifer , Kwiatkowski Kat , de la Vega Lorena Lazo , Mitchell Khalis , Reeder Travis , Siddiqui Javed , Vakil Hana , Johnson D. Bryan , Rhodes Daniel R. 
Published: November 2020

AbstractPurposeTissue-based comprehensive genomic profiling (CGP) is increasingly utilized for treatment selection in patients with advanced solid tumors, however real-world tissue availability may limit widespread implementation. Here we established real-world CGP tissue availability and assessed CGP performance on consecutively received samples.Patients and MethodPost-hoc, non-prespecified analysis of 32,048 consecutive tumor tissue samples received for StrataNGS, a multiplex PCR based-CGP (PCR-CGP) test, as part of an ongoing observational trial (NCT03061305). Tumor tissue sample characteristics and PCR-CGP performance were assessed across all tested tumor samples, including exception samples not meeting minimum input requirements (<20% tumor content [TC], <2mm2 tumor surface area [TSA], DNA or RNA yield <1ng/ul, or specimen age >5yrs). Tests reporting at least one prioritized alteration or meeting all sequencing QC metrics (and ≥20% TC) were considered successful. For prostate carcinoma and lung adenocarcinoma, tests reporting at least one actionable/informative alteration or those meeting all sequencing QC metrics (and ≥20% TC) were considered actionable.ResultsPCR-CGP was attempted in 31,165 of 32,048 (97.2%) consecutively received solid tumor tissue samples. Among the 31,165 tested samples, 10.7% had low (<20%) tumor content (TC) and 58.4% were small (<25mm2 TSA), highlighting the challenging nature of samples received for CGP. Of the 31,101 samples evaluable for input requirements, 8,079 (26.0%) were exceptions not meeting requirements. However, 94.2% of the 31,101 tested samples were successfully reported, including 80.6% of exception samples. Importantly, 80.6% of 1,344 tested prostate carcinomas and 87.8% of 1,144 tested lung adenocarcinomas yielded results informing treatment selection.ConclusionMost real-world tumor tissue samples from patients with advanced cancer desiring CGP are limited, requiring optimized CGP approaches to produce meaningful results. An optimized PCR-CGP test, coupled with an inclusive exception testing policy, delivered reportable results for >94% of samples, potentially expanding the proportion of CGP-testable patients, and thus the impact of biomarker-guided targeted and immunotherapies.
Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment
Authors: Marotz Clarisse , Belda-Ferre Pedro , Ali Farhana , Das Promi , Huang Shi , Cantrell Kalen , Jiang Lingjing , Martino Cameron , Diner Rachel E. , Rahman Gibraan , McDonald Daniel , Armstrong George , Kodera Sho , Donato Sonya , Ecklu-Mensah Gertrude , Gottel Neil , Salas Garcia Mariana C. , Chiang Leslie Y. , Salido Rodolfo A. , Shaffer Justin P. , Bryant MacKenzie , Sanders Karenina , Humphrey Greg , Ackermann Gail , Haiminen Niina , Beck Kristen L. , Kim Ho-Cheol , Carrieri Anna Paola , Parida Laxmi , Vázquez-Baeza Yoshiki , Torriani Francesca J. , Knight Rob , Gilbert Jack A. , Sweeney Daniel A. , Allard Sarah M. 
Published: November 2020

AbstractSynergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context of SARS-CoV-2. We collected 972 samples from hospitalized patients with coronavirus disease 2019 (COVID-19), their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and contextualized the massive microbial diversity in this dataset through meta-analysis of over 20,000 samples. Sixteen percent of surfaces from COVID-19 patient rooms were positive, with the highest prevalence in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples increasingly resembled the patient microbiome over time, SARS-CoV-2 was detected less there (11%). Despite viral surface contamination in almost all patient rooms, no health care workers contracted the disease, suggesting that personal protective equipment was effective in preventing transmissions. SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity across human and surface samples, and higher biomass in floor samples. 16S microbial community profiles allowed for high SARS-CoV-2 classifier accuracy in not only nares, but also forehead, stool, and floor samples. Across distinct microbial profiles, a single amplicon sequence variant from the genus Rothia was highly predictive of SARS-CoV-2 across sample types and had higher prevalence in positive surface and human samples, even compared to samples from patients in another intensive care unit prior to the COVID-19 pandemic. These results suggest that bacterial communities may contribute to viral prevalence both in the host and hospital environment.One Sentence SummaryMicrobial classifier highlights specific taxa predictive of SARS-CoV-2 prevalence across diverse microbial niches in a COVID-19 hospital unit.
Anthropometrics: A forgotten gem in clinical assessment of obesity
Authors: Bhatti R , Warshow U M. , Joumaa M , ElSaban M , Nawaz F , Khamis A H 
Published: November 2020

AbstractBackgroundAccording to World Health Organization (WHO), United Arab Emirates (UAE) has one of the highest prevalence rates of obesity in the Middle East at 34%. There is a paralleled rise in the incidence of related metabolic conditions, particularly type 2 diabetes, metabolic syndrome and non-alcoholic fatty liver disease (NAFLD). Body mass index (BMI) alone is an insufficient marker of abdominal adiposity and addition of waist circumference (WC) can help to assess the cardiometabolic risk.AimTo study the prevalence of obesity related diseases in a multidisciplinary weight management program and determine the relationship to obesity anthropometric indices.MethodsThis is a cross-sectional study conducted at Mediclinic Parkview Hospital in Dubai, UAE. 308 patients have been evaluated from January 2019 until September 2019 as part of a multi-disciplinary weight management program. Key demographics, anthropometrics, and clinical data was analyzed using Statistical Package for Social Sciences software version 25 (SPSS Inc., Chicago, IL).ResultsThree hundred and eight patients taking part in the weight management program were studied. The population was constituted of 103 (33%) males and 205 (67%) females. The mean age was 41 years (±9.6) with a median BMI of 34.5 (±6.7) and 33.7 (±7.8) for males and females respectively. Mean waist circumference was 113.4 cm (±23.3) and 103.5 cm (±16.2), fat percent was 33.7% (±11.6) and 45 (±6.8), fat mass was 41 kg (±15.2) and 41.1 (±14.1), and visceral fat was 6.5 kg (±3.2) and 3.1 (±1.8), for males and females respectively. The population was heterogeneous with 38 nationalities. BMI strongly correlated with waist circumference (male; female, r=0.67; r=0.72) and visceral fat (male; female, r=0.89; r=0.78). Further, waist circumference was significantly associated with risk of diabetes, hypertension, and NAFLD.ConclusionThe study has confirmed the high prevalence rates of obesity related diseases in a private hospital setting in a multinational cohort of obese patients. BMI and waist circumference are the most representative measures of obesity in our population and correlate with abdominal adiposity and obesity related diseases. Further studies will play a part in assessing the benefit of these measures during weight reduction interventions.
Pfs230 yields higher malaria transmission-blocking vaccine activity than Pfs25 in humans but not mice
Authors: Healy Sara A. , Anderson Charles , Swihart Bruce J. , Mwakingwe Agnes , Gabriel Erin E. , Decederfelt Hope , Hobbs Charlotte V. , Rausch Kelly M. , Zhu Daming , Muratova Olga , Herrera Raul , Scaria Puthupparampil V. , MacDonald Nicholas J. , Lambert Lynn E. , Zaidi Irfan , Coelho Camila H. , Renn Jonathan P. , Wu Yimin , Narum David L. , Duffy Patrick E. 
Published: November 2020

AbstractBackgroundVaccines that block human-to-mosquitoPlasmodiumtransmission are needed for malaria eradication and clinical trials have targeted zygote antigen Pfs25 for decades. We reported that a Pfs25 protein-protein conjugate vaccine formulated in alum adjuvant induced significant serum functional activity in both US and Malian adults. However, antibody titers declined rapidly, and transmission-reducing activity required four vaccine doses. Functional immunogenicity and durability must be improved before advancing TBV further in clinical development. We hypothesized that the pre-fertilization protein Pfs230 alone or in combination with Pfs25 would improve functional activity.MethodsTransmission-blocking vaccine candidates based on gamete antigen Pfs230 or Pfs25 were conjugated with Exoprotein A, formulated in Alhydrogel®,and administered to mice, rhesus macaques, and humans. Antibody titers were measured by ELISA and transmission-reducing activity was assess by the Standard Membrane Feeding Assay.ResultsPfs25-EPA/Alhydrogel®and Pfs230D1-EPA/Alhydrogel®induced similar serum functional activity in mice, but Pfs230D1-EPA induced significantly greater activity in rhesus monkeys that was enhanced by complement. In U.S. adults, two vaccine doses induced complement-dependent activity in 4 of 5 Pfs230D1-EPA/Alhydrogel® recipients but no significant activity in five Pfs25-EPA recipients, and combination with Pfs25-EPA did not increase activity over Pfs230D1-EPA alone.ConclusionThe complement-dependent functional immunogenicity of Pfs230D1-EPA represents a significant improvement over Pfs25-EPA. The rhesus model is more predictive of the functional human immune response to Pfs230D1 than is the mouse model.Trial RegistrationClinicalTrials.govNCT02334462FundingThis work was supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, National Institutes of Health.
A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic
Authors: Flynn Michael J. , Snitser Olga , Flynn James , Green Samantha , Yelin Idan , Szwarcwort-Cohen Moran , Kishony Roy , Elowitz Michael B. 
Published: November 2020

AbstractWidespread, frequent testing is essential for curbing the ongoing COVID-19 pandemic. Because its simplicity makes it ideal for widely distributed, high throughput testing, RT-LAMP provides an attractive alternative to RT-qPCR. However, most RT-LAMP protocols require the purification of RNA, a complex and low-throughput bottleneck that has often been subject to reagent supply shortages. Here, we report an optimized RT-LAMP-based SARS-CoV-2 diagnostic protocol for saliva and swab samples. In the protocol we replace RNA purification with a simple sample preparation step using a widely available chelating agent, as well as optimize key protocol parameters. When tested on clinical swab and saliva samples, this assay achieves a limit of detection of 105viral genomes per ml, with sensitivity close to 90% and specificity close to 100%, and takes 45 minutes from sample collection to result, making it well suited for a COVID-19 surveillance program.
The effectiveness of early diagnostic tools for neural lesions in leprosy An observational cohort study
Authors: Cegana Luciano Henrique Vieira , Nardi Susilene Maria Tonelli , Pascoeto Luciana , Paschoal Vania Del Arco 
Published: November 2020

ABSTRACTCegana LHV, Nardi SMT, Pascoeto L, Paschoal VDA. The effectiveness of early diagnostic tools for neural lesions in leprosy. 37p. MANUSCRIPT, 2020. https://doi.org/10.1101/2020.11.19.20234963IntroductionLeprosy can cause different lesions in peripheral nerves and inervatory structures.ObjectivesTo analyse the effectiveness of evaluation protocols used to identify neural lesions in leprosy such as Degree of Physical Disability (DPD), Simplified Neurological Assessment (SNA) and propose to use Neurodynamic Assessment (NDA).MethodDescriptive analytical study, associative, with 27 individuals treated in two outpatient leprosy clinics in São Paulo State, between 2017 and 2019, and 27 individuals from the paired control group. The Mann-Whitney, Multivariate Linear Regression and association between variables and P<0.05 values were used.ResultsThe test that most captured the neurological alterations was the SNA, with 22 (81.5%) in the upper limbs (ULs) and 25 (92.6%) in the lower limbs (LLs), followed by the NDA, with 20 (74.1%) in the ULs and 11 (40.7%) in the LLs. The DPD showed handicap in the hands of 16 (59.2%) individuals and in the feet of 17 (62.9%) individuals, and they have expressed sensitivity. DPD showed agreement with SNA in 21 (77.8%) of the cases in ULs (p=0.010) and 19 (70,4%) of the cases in LLs (p=0.060). DPD and NDA showed that in 19 (70.4%) of the patients evaluated there was concordance of results in ULs (p=0.143); 9 (33.3%) in LLs (p=0.125). SNA and the NDA in the ULs found agreement in 21 (77.8%); 11 (40.7%) (p=0.786) in the LLs.ConclusionThe three assessment instruments are specific and will hardly produce false positive tests. DPD can produce more false negatives than SNA. If there is an instrument to be chosen, it should be the SNA, since it is more sensitive, more accurate and has a less negative likelihood ratio. Neurodynamic tests were positive in 7.4% of individuals while there were still no changes in the SNA; afterwards, these changes appeared.DescriptorsNeural mobilization; Leprosy; Peripheral nerves; Disability; Pain; Physical therapy.
A framework to model global, regional, and national estimates of intimate partner violence
Authors: Maheu-Giroux Mathieu , Sardinha Lynnmarie , Stöckl Heidi , Meyer Sarah , Godin Arnaud , Alexander Monica , García-Moreno Claudia 
Published: November 2020

AbstractBackgroundAccurate and reliable estimates of violence against women statistics form the backbone of monitoring efforts to eliminate these human right violations and public health concerns. Estimating the prevalence of intimate partner violence (IPV) is challenging due to variations in case definition and recall period, surveyed populations, partner definition, level of age disaggregation, and survey representativeness, among others. In this paper, we aim to develop a sound and flexible statistical modeling framework for global, regional, and national IPV statistics.MethodsWe modeled IPV within a Bayesian multilevel modeling framework, accounting for heterogeneity of age groups using age-standardization, and age patterns and time trends using splines functions. Survey comparability is achieved using adjustment factors which are estimated using exact matching and their uncertainty accounted for. Both in-sample and out-of-sample comparisons are used for model validation, including posterior predictive checks. Post-processing of models’ outputs is performed to aggregate estimates at different geographic levels and age groups.ResultsA total of 307 unique studies conducted between 2000-2018, from 154 countries/territories/areas, and totaling nearly 1.8 million unique women responses informed lifetime IPV. Past year IPV had similar number of studies (n=332), countries represented (n=159), and individual responses (n=1.8 million). Roughly half of IPV observations required some adjustments. Posterior predictive checks suggest good model fit to data and out-of-sample comparisons provided reassuring results with small median prediction errors and appropriate coverage of predictions’ intervals.ConclusionsThe proposed modeling framework can pool both national and sub-national surveys, account for heterogeneous age groups and age trends, accommodate different surveyed population, adjust for differences in survey instruments, and efficiently propagate uncertainty to model outputs. By describing this model to reproducible levels of details, the accurate interpretation and responsible use of estimates for global monitoring of violence against women elimination efforts are supported, as part of the Sustainable Development Goals.
Resources allocation explains the differential roles of RBS and promoter strengths in cell mass distribution and optimal protein expression productivity
Authors: Nóbel Fernando , Picó Jesús 
Published: November 2020

AbstractDesign of synthetic genetic circuits without considering the impact of host–circuit interactions results in an inefficient design process and lengthy trial-and-error iterations to appropriately tune the expression levels. Microorganisms have evolved to reach an optimal use of cellular resources. This balance is perturbed by circuit-host interactions resulting from the interaction among the cell environment from which the cell takes substrates, its metabolism, and the needs of exogenous synthetic genetic circuit introduced in the cell host. The resulting competition for common shared cell resources introduces spurious dynamics leading to problems of malfunctioning of the synthetic circuit due to lack of enough cellular resources. Therefore, there is an increasing interest in development of methods for model-based design of synthetic gene circuits considering host-circuit interactions. Here we present a small-size model of gene expression dynamics in bacterial cells accounting for host-circuit interactions. For each gene, the model defines the cellular resources recruitment strength as the key functional coefficient that allows to explain the distribution of resources among the host and the genes of interest and the relationship between the usage of resources and cell growth. This functional coefficient explicitly takes into account the availability of resources and lab-accessible gene characteristics, such as promoter and ribosome binding site (RBS) strengths and capture their interplay with the availability of free cell resources. In spite of its simplicity, the model is able to explain the differential role of promoter and RBS strengths in the distribution of protein mass and the optimal protein expression productivity with remarkable fit to the experimental data from the literature forE. coli. This makes the model amenable for model-based circuit design purposes. Moreover, the model also allows to understand why endogenous ribosomal and non-ribosomal genes have evolved different strategies in the expression space.
Isolation thresholds for curbing SARS-CoV-2 resurgence
Authors: Yakob Laith 
Published: November 2020

SummarySelf-instigated isolation is heavily relied on to curb SARS-CoV-2 transmission. Accounting for uncertainty in the latent and prepatent periods, as well as the proportion of infections that remain asymptomatic, the limits of this intervention at different phases of infection resurgence are estimated. We show that by October 2020, SARS-CoV-2 transmission rates in England had already begun exceeding levels that could be interrupted using this intervention alone, lending support to the second national lockdown on November 5th 2020.