bluuebunny/crossref_metadata_2025_split huggingface dataset:
Video-Based Deep Learning to Detect Dyssynergic Defecation with 3D High-Definition Anorectal Manometry
Authors: Levy Joshua J. , Navas Christopher M. , Chandra Joan A. , Christensen Brock C. , Vaickus Louis J. , Curley Michael , Chey William D. , Baker Jason R. , Shah Eric D. 
Published: December 2021

ABSTRACTBACKGROUND AND AIMSEvaluation for dyssynergia is the most common reason that gastroenterologists refer patients for anorectal manometry, because dyssynergia is amenable to biofeedback by physical therapists. High-definition anorectal manometry (3D-HDAM) is a promising technology to evaluate anorectal physiology, but adoption remains limited by its sheer complexity. We developed a 3D-HDAM deep learning algorithm to evaluate for dyssynergia.METHODSSpatial-temporal data were extracted from consecutive 3D-HDAM studies performed between 2018-2020 at a tertiary institution. The technical procedure and gold standard definition of dyssynergia were based on the London consensus, adapted to the needs of 3D-HDAM technology. Three machine learning models were generated: (1) traditional machine learning informed by conventional anorectal function metrics, (2) deep learning, and (3) a hybrid approach. Diagnostic accuracy was evaluated using bootstrap sampling to calculate area-under-the-curve (AUC). To evaluate overfitting, models were validated by adding 502 simulated defecation maneuvers with diagnostic ambiguity.RESULTS302 3D-HDAM studies representing 1,208 simulated defecation maneuvers were included (average age 55.2 years; 80.5% women). The deep learning model had comparable diagnostic accuracy (AUC=0.91 [95% confidence interval 0.89-0.93]) to traditional (AUC=0.93[0.92-0.95]) and hybrid (AUC=0.96[0.94-0.97]) predictive models in training cohorts. However, the deep learning model handled ambiguous tests more cautiously than other models; the deep learning model was more likely to designate an ambiguous test as inconclusive (odds ratio=4.21[2.78-6.38]) versus traditional/hybrid approaches.CONCLUSIONSBy considering complex spatial-temporal information beyond conventional anorectal function metrics, deep learning on 3D-HDAM technology may enable gastroenterologists to reliably identify and manage dyssynergia in broader practice.
Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2
Authors: Titov Aleksei , Shaykhutdinova Regina , Shcherbakova Olga V. , Serdyuk Yana , Sheetikov Savely A. , Zornikova Ksenia V. , Maleeva Alexandra V. , Khmelevskaya Alexandra , Dianov Dmitry V. , Shakirova Naina T. , Malko Dmitry B. , Shkurnikov Maxim , Nersisyan Stepan , Tonevitsky Alexander , Khamaganova Ekaterina , Ershov Anton V. , Osipova Elena Y. , Nikolaev Ruslan V. , Pershin Dmitry E. , Vedmedskia Viktoria A. , Maschan Mikhail , Ginanova Victoria , Efimov Grigory A. 
Published: December 2021

AbstractThe ongoing COVID-19 pandemic calls for more effective diagnostic tools, and T cell response assessment can serve as an independent indicator of prior COVID-19 exposure while also contributing to a more comprehensive characterization of SARS-CoV-2 immunity. In this study, we systematically assessed the immunogenicity of 118 epitopes with immune cells collected from multiple cohorts of vaccinated, convalescent, and healthy unexposed and SARS-CoV-2 exposed donors. We identified seventy-five immunogenic epitopes, 24 of which were immunodominant. We further confirmed HLA restriction for 49 epitopes, and described association with more than one HLA allele for 14 of these. After excluding two cross-reactive epitopes that generated a response in pre-pandemic samples, we were left with a 73-epitope set that offers excellent diagnostic specificity without losing sensitivity compared to full-length antigens, which evoked a robust cross-reactive response. We subsequently incorporated this set of epitopes into an in vitro diagnostic ‘Corona-T-test’ which achieved a diagnostic accuracy of 95% in a clinical trial. When applied to a cohort of asymptomatic seronegative individuals with a history of prolonged SARS-CoV-2 exposure, this test revealed a lack of specific T cell response combined with strong cross-reactivity to full-length antigens, indicating that abortive infection had occurred in these individuals.
Stabilization of Microbial Communities by Responsive Phenotypic Switching
Authors: Haas Pierre A. , Gutierrez Maria A. , Oliveira Nuno M. , Goldstein Raymond E. 
Published: December 2021

AbstractClonal microbes can switch between different phenotypes and recent theoretical work has shown that stochastic switching between these subpopulations can stabilize microbial communities. This phenotypic switching need not be stochastic, however, but could also be in response to environmental factors, both biotic and abiotic. Here, motivated by the bacterial persistence phenotype, we explore the ecological effects of such responsive switching by analyzing phenotypic switching in response to competing species. We show that the stability of microbial communities with responsive switching differs generically from that of communities with stochastic switching only. To understand the mechanisms by which responsive switching stabilizes coexistence, we go on to analyze simple two-species models. Combining exact results and numerical simulations, we extend the classical stability results for the competition of two species without phenotypic variation to the case in which one species switches, stochastically and responsively, between two phenotypes. In particular, we show that responsive switching can stabilize coexistence even when stochastic switching on its own does not affect the stability of the community.
Antimicrobial resistance determinants in silage
Authors: Nagy Sára Ágnes , Gréta Tóth Adrienn , Papp Márton , Kaplan Selçuk , Solymosi Norbert 
Published: December 2021

ABSTRACTAnimal products may play a role in developing and spreading antimicrobial resistance in several ways. On the one hand, residues of antibiotics not adequately used in animal farming can enter the human body via food. But resistant bacteria may also be present in animal products, which can transfer the antimicrobial resistance genes (ARG) to the bacteria in the consumer’s body by horizontal gene transfer. As previous studies have shown that fermented foods have a meaningful ARG content, it is indicated that such genes may also be present in silage used as mass feed in the cattle sector. In our study, we aspired to answer what ARGs occur in silage and what mobility characteristics they have? For this purpose, we have analyzed bioinformatically 52 freely available deep sequenced silage samples from shotgun metagenome next-generation sequencing. A total of 17 perfect matched ARGs occurred 55 times in the samples. More than half of these ARGs are mobile because they can be linked to integrative mobile genetic elements, prophages or plasmids. Our results point to a neglected but substantial ARG source in the food chain.
Continual reelin signaling by the prime neurogenic niche of the adult brain
Authors: Pérez-Martínez F. Javier , Cifuentes Manuel , Luque Juan M. 
Published: December 2021

SummaryDuring development reelin sets the pace of neocortical neurogenesis enabling in turn newborn neurons to migrate, but whether and, if so, how reelin signaling affects the adult neurogenic niches remains uncertain. We show that reelin signaling, resulting in Dab1 phosphorylation, occurs in the ependymal-subependymal zone (EZ/SEZ) of the lateral ventricles where, along with its associated rostral migratory stream (RMS), the highest density of functional ApoER2 accumulates. Mice deficient for reelin, ApoER2 or Dab1 exhibit enlarged ventricles and dysplastic RMS. Moreover, while the conditional ablation of Dab1 in neural progenitor cells (NPCs) enlarges the ventricles and impairs neuroblasts clearance from the SEZ, the transgenic misexpression of reelin in NPCs of reelin-deficient mice normalizes the ventricular lumen and the density of ependymal cilia, ameliorating in turn neuroblasts migration; consistently, intraventricular infusion of reelin reroutes neuroblasts. These results demonstrate that reelin signaling persists sustaining the germinal niche of the lateral ventricles and influencing neuroblasts migration in the adult brain.
Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces
Authors: Lubin Joseph H. , Markosian Christopher , Balamurugan D. , Pasqualini Renata , Arap Wadih , Burley Stephen K. , Khare Sagar D. 
Published: December 2021

AbstractThere is enormous ongoing interest in characterizing the binding properties of the SARS-CoV-2 Omicron Variant of Concern (VOC) (B.1.1.529), which continues to spread towards potential dominance worldwide. To aid these studies, based on the wealth of available structural information about several SARS-CoV-2 variants in the Protein Data Bank (PDB) and a modeling pipeline we have previously developed for tracking the ongoing global evolution of SARS-CoV-2 proteins, we provide a set of computed structural models (henceforth models) of the Omicron VOC receptor-binding domain (omRBD) bound to its corresponding receptor Angiotensin-Converting Enzyme (ACE2) and a variety of therapeutic entities, including neutralizing and therapeutic antibodies targeting previously-detected viral strains. We generated bound omRBD models using both experimentally-determined structures in the PDB as well as machine learningbased structure predictions as starting points. Examination of ACE2-bound omRBD models reveals an interdigitated multi-residue interaction network formed by omRBD-specific substituted residues (R493, S496, Y501, R498) and ACE2 residues at the interface, which was not present in the original Wuhan-Hu-1 RBD-ACE2 complex. Emergence of this interaction network suggests optimization of a key region of the binding interface, and positive cooperativity among various sites of residue substitutions in omRBD mediating ACE2 binding. Examination of neutralizing antibody complexes for Barnes Class 1 and Class 2 antibodies modeled with omRBD highlights an overall loss of interfacial interactions (with gain of new interactions in rare cases) mediated by substituted residues. Many of these substitutions have previously been found to independently dampen or even ablate antibody binding, and perhaps mediate antibody-mediated neutralization escape (e.g., K417N). We observe little compensation of corresponding interaction loss at interfaces when potential escape substitutions occur in combination. A few selected antibodies (e.g., Barnes Class 3 S309), however, feature largely unaltered or modestly affected protein-protein interfaces. While we stress that only qualitative insights can be obtained directly from our models at this time, we anticipate that they can provide starting points for more detailed and quantitative computational characterization, and, if needed, redesign of monoclonal antibodies for targeting the Omicron VOC Spike protein. In the broader context, the computational pipeline we developed provides a framework for rapidly and efficiently generating retrospective and prospective models for other novel variants of SARS-CoV-2 bound to entities of virological and therapeutic interest, in the setting of a global pandemic.
Optimizing the energy bandwidth for transmission full-field X-ray microscopy experiments
Authors: Storm Malte , Döring Florian , Marathe Shashidhara , Cipiccia Silvia , David Christian , Rau Christoph 
Published: December 2021

Full-field transmission X-ray microscopy (TXM) is a very potent high-resolution X-ray imaging technique. However, it is challenging to achieve fast acquisitions because of the limited efficiency of the optics. Using a broader energy bandwidth, for example using a multilayer monochromator, directly increases the flux in the experiment. The advantage of more counts needs to be weighed against a deterioration in achievable resolution because focusing optics show chromatic aberrations. This study presents theoretical considerations of how much the resolution is affected by an increase in bandwidth as well as measurements at different energy bandwidths (ΔE/E = 0.013%, 0.27%, 0.63%) and the impact on achievable resolution. It is shown that using a multilayer monochromator instead of a classical silicon double-crystal monochromator can increase the flux by an order of magnitude with only a limited effect on the resolution.
Scaling up Sirohi: can women empowerment and sustainability drive a luxury brand?
Authors: Sondhi Neena , Basu Rituparna 
Published: December 2021

Learning outcomes
The case offers a unique opportunity to understand the market dynamics of a young luxury brand that aspires to empower women and pursue the broader goal of marketing sustainability in an emerging market. The discussion would enable learners to conduct environmental analysis and assess implications of crisis (current pandemic) on business, understand the marketing mix implications for a firm with societal orientation, learn to design effective brand positioning strategies and plan social and market driven brand strategies to ensure sustainable growth.

Case overview/synopsis
Gauri Malik, an investment banker-turned-social entrepreneur, forayed into the luxury home décor and furniture market with Sirohi, in 2019. In a market driven by exclusivity and design appeal, the brand had sustainability at its core. Malik worked with 200 women, from a conservative rural base in India to create traditional products that were hand-made with recycled natural fibres and upcycled plastic wastes. Driven by the goal of securing the livelihood for a larger group of women artisans, Malik wanted to scale up from 350 to 5000 products in the next five years. Hence, for materializing her ambitious plans she sought answers to- Could her home-trained women artisans deliver the promise of quality and finesse to support Sirohi scale up as a luxury brand? While it was extremely critical for Sirohi to have an articulated image-she wondered if the parallel focus on the up-market luxury brand image and sustainability-create competitive advantage or lead to diffused positioning?

Complexity academic level
Classified as MODERATE in terms of difficulty level, the case can be effectively used in post-graduate programmes for foundation courses on Marketing Management, elective courses on Brand Management or Sustainability Marketing.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 8: Marketing.
Research on strengthening stone arch bridge with CFRP rebars
Authors: Zhang Kexin , Li Dachao , Shen Xinyuan , Hou Wenyu , Li Yanfeng , Xue Xingwei 
Published: December 2021

PurposeThis paper aims to describe carbon fiber reinforced plastics (CFRP) bars as a way to strengthen a 40-year-old stone arch bridge. To investigate effectiveness of the strengthening method, fielding-load tests were carried out before and after strengthening.Design/methodology/approachHigh-strength CFRP bars with minor radius, high tensile strain and good corrosion resistance were used in this reinforcement. The construction process for strengthening with CFRP bars – including CFRP bars cutting, crack grouting, original structural surface treatment, implant drilling, CFRP bars installation and pouring mortar – was described. Ultimate bearing capacity of the bridge after strengthening was discussed.FindingsThe results of concrete stress and deflection show that the strength and stiffness of the strengthened bridge are improved. The strengthened way with CFRP bars is feasible and effective.Originality/valueThis paper describes CFRP bars as a way to strengthen a 40-year-old stone arch bridge.
A dual-branch balance saliency model based on discriminative feature for fabric defect detection
Authors: Liu Zhoufeng , Wang Menghan , Li Chunlei , Ding Shumin , Li Bicao 
Published: December 2021

PurposeThe purpose of this paper is to focus on the design of a dual-branch balance saliency model based on fully convolutional network (FCN) for automatic fabric defect detection, and improve quality control in textile manufacturing.Design/methodology/approachThis paper proposed a dual-branch balance saliency model based on discriminative feature for fabric defect detection. A saliency branch is firstly designed to address the problems of scale variation and contextual information integration, which is realized through the cooperation of a multi-scale discriminative feature extraction module (MDFEM) and a bidirectional stage-wise integration module (BSIM). These modules are respectively adopted to extract multi-scale discriminative context information and enrich the contextual information of features at each stage. In addition, another branch is proposed to balance the network, in which a bootstrap refinement module (BRM) is trained to guide the restoration of feature details.FindingsTo evaluate the performance of the proposed network, we conduct extensive experiments, and the experimental results demonstrate that the proposed method outperforms state-of-the-art (SOTA) approaches on seven evaluation metrics. We also conduct adequate ablation analyses that provide a full understanding of the design principles of the proposed method.Originality/valueThe dual-branch balance saliency model was proposed and applied into the fabric defect detection. The qualitative and quantitative experimental results show the effectiveness of the detection method. Therefore, the proposed method can be used for accurate fabric defect detection and even surface defect detection of other industrial products.
Gulf property damage, housing price trends and US bankruptcy filings
Authors: Brotman Billie Ann , Katzman Brett 
Published: December 2021

Purpose
This paper aims to examine potential causes of bankruptcy as they relate to hurricane damage. Investigate whether hurricanes result in personal bankruptcy filings due to real property damages. Strengthen existing descriptive results by using fully modified ordinary least squares (FMOLS).

Design/methodology/approach
Lagged FMOLS model is used with data from states that suffered hurricane damage between 2000 through 2020. FMOLS controls for various financial distresses that can cause bankruptcy filings.

Findings
Bankruptcy is usually filed for within one year of a hurricane. Changes in house prices and hurricane severity were significant indicators of bankruptcy filings. However, the divorce rate, commonly thought of as a primary reason for bankruptcy, is insignificant.

Research limitations/implications
Data was available on a state level for the independent variables. Hurricane damage needed to be financially significant enough for inland flooding to be measurable and influential.

Practical implications
Establishes that financial distress comes from several sources, not just home damage. Financial distress is highly correlated with whether a home was insured. Divorce does not cause bankruptcy filings.

Social implications
Federal flood insurance programs should be reexamined. Having a broader all-risk homeowner policy could reduce the number of households that file for bankruptcy after a hurricane.

Originality/value
Existing research uses descriptive statistics and obtains mixed findings regarding the association between hurricane damage and bankruptcy filings. The FMOLS approach provides clarity about this association.
Assessing the macro and micro elements of the Akbarieh World Heritage Garden using participant observer method in a continuous/stop-motion
Authors: Khalilnezhad Mohammad Reza , Kopec Dak 
Published: December 2021

PurposeThis study aims to assess each of the seven segments of the Akbarieh Garden as the World Heritage Cultural Landscape. First, we wanted to identify the macro elements that dominated one's perception within each area. Then, we wanted to identify the micro elements that support the vista in its entirety.Design/methodology/approachTo acquire data, we used a Participant Observer (PO) method as part of a Continuous/Stop-Motion (CSM) procedure. The identification of macro elements came from retrospective recollections derived from the continuous walk method—the stop-walk method allowed for the identification of micro elements. The data gained from this method is then used to understand how one interprets and responds to large—multi-segmented sites such as the Akbarieh Garden.FindingsThe results of this study show the Continuous/Stop-Motion method yielded predictable results with macro elements and elements of interest being easily recalled. However, the use of photographing for the stop-walk method revealed a similar focus on the macro element. We had hypothesized that the micro elements would be the elements of fascination and discovered when the person remained in the area to photograph scenes of interest. However, the PO photographed the macro elements. It wasn't until the post photo analysis that the PO identified some of the micro elements would be the elements of fascination and discovered when the person remained in the area to photograph scenes of interest. However, the PO photographed the macro elements. It wasn't until the post photo analysis that the PO identified some of the micro elements. The post photo discoveries suggest that real-time experience of micro elements is undervalued.Originality/valueThere is no general discussion on this topic yet amongst professionals. The initiative of the Participant Observer (PO) method as a tool for perception the historic gardens and landscapes identified that gap and its related necessity to provide guidance. As is true for exploratory studies, these results provide a foundation for further study. The use of the Continuous/Stop-Motion method was ideal for this study.
Implementing Islamic principles and values in public budgeting: a battle of mindset
Authors: Farhana Intan , Markham Clare , Basri Hasan 
Published: December 2021

PurposeThis paper aims to analyse the implementation of Islamic principles and values within the budgetary management of one of Indonesia’s local governments, that of Aceh provincial government. The authors investigate the extent of Islamic teachings in Aceh’s public budgeting to gain an understanding of the challenges in implementing such ideas in practice.Design/methodology/approachTo investigate these issues, the authors used a qualitative interpretive approach in this study, gathering written materials related to the budgeting process and conducting 19 interviews with local government officials, politicians, scholars and a corruption watchdog. Data was manually coded and thematically analysed.FindingsIn this study, the authors find that the budgetary management problems Aceh provincial government faces (including poor resource allocation, budget delays and poor accountability and transparency) indicate unsatisfactory performance in incorporating Islamic principles and values into government. The authors argue that a key challenge to a more complete implementation is that the Acehnese’ perspectives of Sharī’ah and its enactment remain limited to particular aspects, such as criminal law, rituals and symbols, and are not extended to wider governance and budgetary practices.Practical implicationsThe findings are likely to be of interest to policymakers and those who hold them to account, in a region/country where Islamic values and principles largely influence the government and social affairs. They indicate that a broader conception of Sharī’ah would facilitate a more thorough implementation of Islamic principles and values within public budgeting.Originality/valueThis study is one of a handful of studies exploring Islamic public budgeting, with its originality lying in the investigation of the challenges faced in implementing Islamic principles in government budgeting.