bluuebunny/crossref_metadata_2025 huggingface dataset:
Urine-derived stem cells: applications in skin, bone and articular cartilage repair
Authors: Zhang Wenqian , Hu Jungen , Huang Yizhou , Wu Chenyu , Xie Huiqi
Published: September 2021

As an emerging type of adult stem cell featuring non-invasive acquisition, urine-derived stem cells (USCs) have shown great potential for applications in tissue engineering and regenerative medicine. With a growing amount of research on the topic, the effectiveness of USCs in various disease models has been shown and the underlying mechanisms have also been explored, though many aspects still remain unclear. In this review, we aim to provide an up-to-date overview of the biological characteristics of USCs and their applications in skin, bone and articular cartilage repair. In addition to the identification procedure of USCs, we also summarize current knowledge of the underlying repair mechanisms and application modes of USCs. Potential concerns and perspectives have also been summarized.
News Fixers at the Digital Interface: Precarious Labor and International Journalism in the 21st Century
Authors: Palmer Lindsay
Published: September 2021

This article conducts a discursive interface analysis of World Fixer, the most visible online platform currently connecting foreign correspondents with local news workers who can help them translate interviews, navigate unfamiliar places, and stay safe in the field. Placing Johanna Drucker’s theory of the digital interface into conversation with the critical frameworks found in global communication studies, anti-colonial theory, and anti-racist communication scholarship, the goal is to illuminate both the opportunities that the World Fixer site provides its users, as well as the inequalities that the website still perpetuates.
EEG Spatiotemporal Patterns Underlying Self-other Voice Discrimination
Authors: Iannotti Giannina Rita , Orepic Pavo , Brunet Denis , Koenig Thomas , Alcoba-Banqueri Sixto , Garin Dorian F A , Schaller Karl , Blanke Olaf , Michel Christoph M
Published: September 2021

There is growing evidence showing that the representation of the human “self” recruits special systems across different functions and modalities. Compared to self-face and self-body representations, few studies have investigated neural underpinnings specific to self-voice. Moreover, self-voice stimuli in those studies were consistently presented through air and lacking bone conduction, rendering the sound of self-voice stimuli different to the self-voice heard during natural speech. Here, we combined psychophysics, voice-morphing technology, and high-density EEG in order to identify the spatiotemporal patterns underlying self-other voice discrimination (SOVD) in a population of 26 healthy participants, both with air- and bone-conducted stimuli. We identified a self-voice-specific EEG topographic map occurring around 345 ms post-stimulus and activating a network involving insula, cingulate cortex, and medial temporal lobe structures. Occurrence of this map was modulated both with SOVD task performance and bone conduction. Specifically, the better participants performed at SOVD task, the less frequently they activated this network. In addition, the same network was recruited less frequently with bone conduction, which, accordingly, increased the SOVD task performance. This work could have an important clinical impact. Indeed, it reveals neural correlates of SOVD impairments, believed to account for auditory-verbal hallucinations, a common and highly distressing psychiatric symptom.
In Utero MRI Identifies Impaired Second Trimester Subplate Growth in Fetuses with Congenital Heart Disease
Authors: Wu Yao , Lu Yuan-Chiao , Kapse Kushal , Jacobs Marni , Andescavage Nickie , Donofrio Mary T , Lopez Catherine , Quistorff Jessica Lynn , Vezina Gilbert , Krishnan Anita , du Plessis Adré J , Limperopoulos Catherine
Published: September 2021

The subplate is a transient brain structure which plays a key role in the maturation of the cerebral cortex. Altered brain growth and cortical development have been suggested in fetuses with complex congenital heart disease (CHD) in the third trimester. However, at an earlier gestation, the putative role of the subplate in altered brain development in CHD fetuses is poorly understood. This study aims to examine subplate growth (i.e., volume and thickness) and its relationship to cortical sulcal development in CHD fetuses compared with healthy fetuses by using 3D reconstructed fetal magnetic resonance imaging. We studied 260 fetuses, including 100 CHD fetuses (22.3–32 gestational weeks) and 160 healthy fetuses (19.6–31.9 gestational weeks). Compared with healthy fetuses, CHD fetuses had 1) decreased global and regional subplate volumes and 2) decreased subplate thickness in the right hemisphere overall, in frontal and temporal lobes, and insula. Compared with fetuses with two-ventricle CHD, those with single-ventricle CHD had reduced subplate volume and thickness in right occipital and temporal lobes. Finally, impaired subplate growth was associated with disturbances in cortical sulcal development in CHD fetuses. These findings suggested a potential mechanistic pathway and early biomarker for the third-trimester failure of brain development in fetuses with complex CHD.

Significance Statement

Our findings provide an early biomarker for brain maturational failure in fetuses with congenital heart disease, which may guide the development of future prenatal interventions aimed at reducing neurological compromise of prenatal origin in this high-risk population.
Minimally Invasive Tissue Sampling as an Alternative to Complete Diagnostic Autopsies in the Context of Epidemic Outbreaks and Pandemics: The Example of Coronavirus Disease 2019 (COVID-19)
Authors: Bassat Quique , Varo Rosauro , Hurtado Juan Carlos , Marimon Lorena , Ferrando Melania , Ismail Mamudo R , Carrilho Carla , Fernandes Fabiola , Castro Pedro , Maixenchs Maria , Rodrigo-Calvo Maria Teresa , Guerrero José , Martínez Antonio , Lacerda Marcus V G , Mandomando Inacio , Menéndez Clara , Martinez Miguel J , Ordi Jaume , Rakislova Natalia
Published: September 2021

Background

Infectious diseases’ outbreak investigation requires, by definition, conducting a thorough epidemiological assessment while simultaneously obtaining biological samples for an adequate screening of potential responsible pathogens. Complete autopsies remain the gold-standard approach for cause-of-death evaluation and characterization of emerging diseases. However, for highly transmissible infections with a significant associated lethality, such as COVID-19, complete autopsies are seldom performed due to biosafety challenges, especially in low-resource settings. Minimally invasive tissue sampling (MITS) is a validated new approach based on obtaining postmortem samples from key organs and body fluids, a procedure that does not require advanced biosafety measures or a special autopsy room.

Methods

We aimed to review the use of MITS or similar procedures for outbreak investigation up to 27 March 2021 and their performance for evaluating COVID-19 deaths.

Results

After a literature review, we analyzed in detail the results of 20 studies conducted at international sites, whereby 216 COVID-19–related deaths were investigated. MITS provided a general and more granular understanding of the pathophysiological changes secondary to the infection and high-quality samples where the extent and degree of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–related damage could be evaluated.

Conclusions

MITS is a useful addition in the investigation and surveillance of infections occurring in outbreaks or epidemics. Its less invasive nature makes the tool more acceptable and feasible and reduces the risk of procedure-associated contagion, using basic biosafety measures. Standardized approaches protocolizing which samples should be collected—and under which exact biosafety measures—are necessary to facilitate and expand its use globally.
A Multi-Objective Randomly Updated Beetle Swarm and Multi-Verse Optimization for Brain Tumor Segmentation and Classification
Authors: Kumar Katukuri Arun , Boda Ravi
Published: September 2021

This paper plans to develop the optimal brain tumor classification model with diverse intelligent methods. The main phases of the proposed model are ‘(a) image pre-processing, (b) skull stripping, (c) tumor segmentation, (d) feature extraction and (e) classification’. At first, pre-processing of the image is performed by converting the image from red green blue to gray followed by median filtering. Further, skull stripping is done for removing the extra-meningeal tissue from the head image, which is done by Otsu thresholding. As the main contribution, the tumor segmentation is done by the optimized threshold-based tumor segmentation using multi-objective randomly updated beetle swarm and multi-verse optimization (RBS-MVO). The objective constraints considered for the segmentation of the tumor is entropy and variance. Next, the feature extraction techniques like gray level co-occurrence matrix, local binary pattern and gray-level run length matrix is accomplished to extract the set of features. The classification side uses the combination of neural network (NN) and deep learning model called convolutional neural network (CNN) for tumor classification. The extracted features are subjected to NN, and the segmented image is taken as input to CNN. In addition, the weight function of NN and hidden neurons of CNN is optimized by the RBS-MVO.
The utility of implantable loop recorders in patient management: an age- and indication-stratified study in the outpatient-implant era
Authors: Sanghvi Mihir M , Jones Daniel M , Kalindjian Jeremy , Monkhouse Christopher , Providencia Rui , Schilling Richard J , Ahluwalia Nikhil , Earley Mark J , Finlay Malcolm
Published: September 2021

Aim

Implantable loop recorders (ILRs) are now routinely implanted for long-term cardiac monitoring in the clinical setting. The aim of this study was to examine the real-world performance of these devices focusing on the management changes made in response to ILR-recorded data.

Methods and results

This was a single-centre, prospective observational study of consecutive patients undergoing ILR implantation. All patients who underwent implantation of a Medtronic Reveal LINQ device from September 2017 to June 2019 at Barts Heart Centre were included. Five hundred and one patients were included. Three hundred and two (60%) patients underwent ILR implantation for an indication of pre-syncope/syncope, 96 (19%) for palpitations, 72 (14%) for atrial fibrillation (AF) detection with a history of cryptogenic stroke, and 31 (6%) for high risk of serious cardiac arrhythmia. The primary outcome of this study was that an ILR-derived diagnosis altered management in 110 patients (22%). Secondary outcomes concerned subgroup analyses by indication: in patients who presented with syncope/pre-syncope, a change in management resulting from ILR data was positively associated with age [hazard ratio (HR) 1.04, 95% confidence interval 1.02–1.06; P < 0.001] and negatively associated with a normal electrocardiogram at baseline (HR 0.54 [0.31–0.93]; P = 0.03). Few patients (1/57, 2%) aged <40 years in this group underwent device implantation, compared to 19/62 patients (31%) aged 75 years and over (P = 0.0024). Out of 183 (12%) patients, 22 in the 40–74 age range had a device implanted. Among patients who underwent ILR insertion following cryptogenic stroke, 13/72 (18%) had AF detected, leading to a decision to commence anticoagulation.

Conclusion

These results inform the utility of ILR in the clinical setting. Diagnoses provided by ILR that lead to changes in management are rare in patients under age 40, particularly following syncope, pre-syncope, or palpitations. In older patients, new diagnoses are frequently made and trigger important changes in treatment.
The evidence for the implantable loop recorder in patients with inherited arrhythmia syndromes: a review of the literature
Authors: Balfe Christopher , Durand Rory , Crinion Derek , Ward Deirdre , Sheahan Richard
Published: September 2021

Risk stratification of patients with inherited arrhythmia syndromes (IASs) can be challenging. Recent guidelines acknowledge a place for considering the implantable loop recorder (ILR) to outrule malignant arrhythmia as a cause of syncope in certain inherited arrhythmia patients who are at low risk of sudden cardiac death. In this comprehensive literature review, we evaluate the available evidence for the use of the ILR in the IASs and in relatives of victims of sudden arrhythmic death syndrome.
Challenging German physical education teacher educators’ health-related beliefs through Cooperative Planning
Authors: Hapke Julia , Töpfer Clemens , Lohmann Julia
Published: September 2021

Physical education teacher educators’ health-related beliefs can impact public health. An interactive knowledge-to-action approach, such as Cooperative Planning, might challenge the health-related beliefs of physical education teacher educators, thus contributing to innovation in teacher education. We investigated what health-related beliefs physical education teacher educators had before a Cooperative Planning intervention, how these developed throughout the intervention and how teacher educators’ perceptions of Cooperative Planning can explain the identified changes and continuities. We established two Cooperative Planning groups that included physical education teacher educators (university lecturers and teacher trainers), researchers, study course coordinators and prospective teachers. The data of 13 teacher educators were collected before (t0) and after (t1) the Cooperative Planning using two methods: observations of teaching practice and interviews. The data analysis was based on the following categories: (i) epistemic beliefs about health (e.g. salutogenic understanding), (ii) beliefs about the health topic in physical education (e.g. health-related knowledge and understanding), (iii) beliefs about the health topic in physical education teacher education (e.g. health-related pedagogical content knowledge) and (iv) process-related beliefs about Cooperative Planning. The findings revealed that teacher educators’ health-related beliefs were rather stable but could be challenged through a Cooperative Planning intervention. Epistemic beliefs about health remained, whereas more practice-related beliefs about the health topic in physical education and physical education teacher education changed in individual ways. Here, a change in beliefs was more likely when the participants were open to change and when Cooperative Planning offered opportunities to engage in concrete lesson planning.
Availability, supply, and aggregation of prey (Calanusspp.) in foraging areas of the North Atlantic right whale (Eubalaena glacialis)
Authors: Sorochan K A , Plourde S , Baumgartner M F , Johnson C L
Published: September 2021

The North Atlantic right whale (NARW), Eubalaena glacialis, resides primarily on western North Atlantic continental shelves where this endangered species is susceptible to vessel strike and entanglement in fishing gear. Mitigation of these threats is dependent on the ability to predict variations in NARW occurrence. North of the Mid-Atlantic Bight, the distribution of NARWs is influenced by their prey, mainly copepods of the genus Calanus. We review factors that promote suitable foraging habitat from areas where NARWs have been observed feeding. We then synthesize our findings within a conceptual framework in which availability (i.e. shallow prey depth), supply, and aggregation of prey occur together to facilitate suitable foraging habitat. By definition, the depth of prey on the shelf is constrained to ≤200 m and other mechanisms may occur locally that further enhance prey availability. Enhanced production of prey occurs in coastal currents, which transport the copepods to NARW foraging areas. Prey concentrating mechanisms are not well-characterized. Information gaps that impede rapid and dynamic prediction of suitable foraging habitat include limited data on the spatial and temporal variation of prey and environmental conditions at local scales (i.e. 0.1–1 km), motility of prey, and diving behaviour of NARWs.
Model-based geostatistics enables more precise estimates of neglected tropical-disease prevalence in elimination settings: mapping trachoma prevalence in Ethiopia
Authors: Amoah Benjamin , Fronterre Claudio , Johnson Olatunji , Dejene Michael , Seife Fikre , Negussu Nebiyu , Bakhtiari Ana , Harding-Esch Emma M , Giorgi Emanuele , Solomon Anthony W , Diggle Peter J
Published: September 2021

Background

As the prevalences of neglected tropical diseases reduce to low levels in some countries, policymakers require precise disease estimates to decide whether the set public health targets have been met. At low prevalence levels, traditional statistical methods produce imprecise estimates. More modern geospatial statistical methods can deliver the required level of precision for accurate decision-making.

Methods

Using spatially referenced data from 3567 cluster locations in Ethiopia in the years 2017, 2018 and 2019, we developed a geostatistical model to estimate the prevalence of trachomatous trichiasis and to calculate the probability that the trachomatous trichiasis component of the elimination of trachoma as a public health problem has already been achieved for each of 482 evaluation units. We also compared the precision of traditional and geostatistical approaches by the ratios of the lengths of their 95% predictive intervals.

Results

The elimination threshold of trachomatous trichiasis (prevalence ≤ 0.2% in individuals aged ≥15 years) is met with a probability of 0.9 or more in 8 out of the 482 evaluation units assessed, and with a probability of ≤0.1 in 469 evaluation units. For the remaining five evaluation units, the probability of elimination is between 0.45 and 0.65. Prevalence estimates were, on average, 10 times more precise than estimates obtained using the traditional approach.

Conclusions

By accounting for and exploiting spatial correlation in the prevalence data, we achieved remarkably improved precision of prevalence estimates compared with the traditional approach. The geostatistical approach also delivers predictions for unsampled evaluation units that are geographically close to sampled evaluation units.
Nonlinear Diffusion in Transparent Media
Authors: Giacomelli Lorenzo , Moll Salvador , Petitta Francesco
Published: September 2021

We consider a prototypical nonlinear parabolic equation whose flux has three distinguished features: it is nonlinear with respect to both the unknown and its gradient, it is homogeneous, and it depends only on the direction of the gradient. For such equation, we obtain existence and uniqueness of entropy solutions to the Dirichlet problem, the homogeneous Neumann problem, and the Cauchy problem. Qualitative properties of solutions, such as finite speed of propagation and the occurrence of waiting-time phenomena, with sharp bounds, are shown. We also discuss the formation of jump discontinuities both at the boundary of the solutions’ support and in the bulk.
Correlates of Protection for Cholera
Authors: Iyer Anita S , Harris Jason B
Published: September 2021

A correlate of protection (CoP) is a measured adaptive immune response to vaccination or infection that is associated with protection against disease. However, the degree to which a CoP can serve as a surrogate end point for vaccine efficacy should depend on the robustness of this association. While cholera toxin is a dominant target of the human antibody response to Vibrio cholerae infection, antitoxin responses are not associated with long-term immunity, and are not effective CoPs for cholera. Instead, protection appears to be mediated by functional antibodies that target the O-polysaccharide coated V. cholerae outer membrane. Vibriocidal antibodies, which are complement-dependent bactericidal antibodies, remain the most accepted CoP for cholera and are used as surrogate end points in some vaccine studies. However, the association between vibriocidal antibody titers and immunity is not absolute, and they are unlikely to reflect a mechanistic correlate of protection against cholera.
Antibiotic stewardship in direct-to-consumer telemedicine: translating interventions into the virtual realm
Authors: Li Lucy X , Szymczak Julia E , Keller Sara C
Published: September 2021

Direct-to-consumer (DTC) telemedicine is an increasingly popular modality for delivery of medical care via a virtual platform. As most DTC telemedicine visits focus on infection-related complaints, there is growing concern about the magnitude of antibiotic use associated with this setting. However, there is limited scholarship regarding adapting and implementing antibiotic stewardship principles in this setting as most efforts have been focused on hospitals with more recent work in long-term care facilities and primary care settings. We discuss utilizing the core elements for outpatient antibiotic stewardship as a framework for DTC antibiotic stewardship efforts moving forward.
Recommendation Reversals in Gastroenterology Clinical Practice Guidelines
Authors: Gholami Reza , Khan Rishad , Ramkissoon Anushka , Alabdulqader Abdulrahman , Gimpaya Nikko , Bansal Rishi , Scaffidi Michael A , Prasad Vinay , Detsky Allan S , Baker Jeffrey P , Grover Samir C
Published: September 2021

Background

Recommendations in clinical practice guidelines (CPGs) may be reversed when evidence emerges to show they are futile or unsafe. In this study, we identified and characterized recommendation reversals in gastroenterology CPGs.

Methods

We searched CPGs published by 20 gastroenterology societies from January 1990 to December 2019. We included guidelines which had at least two iterations of the same topic. We defined reversals as when (a) the more recent iteration of a CPG recommends against a specific practice that was previously recommend in an earlier iteration of a CPG from the same body, and (b) the recommendation in the previous iteration of the CPG is not replaced by a new diagnostic or therapeutic recommendation in the more recent iteration of the CPG. The primary outcome was the number of recommendation reversals. Secondary outcomes included the strength of recommendations and quality of evidence cited for reversals.

Results

Twenty societies published 1022 CPGs from 1990 to 2019. Our sample for analysis included 129 unique CPGs. There were 11 recommendation reversals from 10 guidelines. New evidence was presented for 10 recommendation reversals. Meta-analyses were cited for two reversals, and randomized controlled trials (RCTs) for seven reversals. Recommendations were stronger after the reversal for three cases, weaker in two cases, and of similar strength in three cases. We were unable to compare recommendation strengths for three reversals.

Conclusion

Recommendation reversals in gastroenterology CPGs are uncommon but highlight low value or harmful practices.
When is Offspring Viability Fitness a Measure of Paternal Fitness and When is it not?
Authors: Fitzpatrick Courtney L , Wade Michael J
Published: September 2021

We use population genetics to model the evolution of a gene with an indirect effect owing to paternal care and with a second pleiotropic, direct effect on offspring viability. We use the model to illustrate how the common empirical practice of considering offspring viability as a component of parent fitness can confound a gene’s direct and indirect fitness effects. We investigate when this confounding results in a distorted picture of overall evolution and when it does not. We find that the practice has no effect on mean fitness, W, but it does have an effect on the dynamics of gene frequency change, ∆q. We also find that, for some regions of parameter space associated with fitness trade-offs, the distortion is not only quantitative but also qualitative, obscuring the direction of gene frequency change. Because it affects the evolutionary dynamics, it also affects the expected amount of genetic variation at mutation-selection balance, an important consideration in molecular evolution. We discuss empirical techniques for separating direct from indirect effects and how field studies measuring the value of male paternal care might be improved by using them.
Reassessing the Legislative Veto: The Statutory President, Foreign Affairs, and Congressional Workarounds
Authors: Bradley Curtis A
Published: September 2021

A chief reason that the President is insufficiently constrained when exercising statutorily-delegated power, it is claimed, is the Supreme Court’s disallowance of legislative vetoes in its decision in INS v. Chadha, a claim that intensified during the Trump administration. This article challenges this account, arguing that the availability of the legislative veto was less important before Chadha to congressional-executive relations than legal scholars commonly assume, and that, to the extent that the legislative veto was (or would have become) important for checking some exercises of statutorily-delegated authority, Congress has developed a host of effective workarounds in the years since Chadha.
Treatment Patterns, Outcomes, and Costs Associated With Localized Upper Tract Urothelial Carcinoma
Authors: Fero Katherine E , Shan Yong , Lec Patrick M , Sharma Vidit , Srinivasan Aditya , Movva Giri , Baillargeon Jacques , Chamie Karim , Williams Stephen B
Published: September 2021

Background

Upper tract urothelial carcinoma (UTUC) is a heterogeneous disease that presents a clinical management challenge for the urologic surgeon. We assessed treatment patterns, costs, and survival outcomes among patients with nonmetastatic UTUC.

Methods

We identified 4114 patients diagnosed with nonmetastatic UTUC from 2004 to 2013 in the Survival Epidemiology, and End Results–Medicare population-based database. Patients were stratified into low- or high-risk disease groups. Median total costs from 30 days prior to diagnosis through 365 days after diagnosis were compared between groups. Overall and cancer-specific survival were evaluated using Cox proportional hazards regression. All statistical tests were 2-sided.

Results

After risk stratification, 1027 (24.9%) and 3087 (75.0%) patients were classified into low- vs high-risk UTUC groups. Most patients underwent at least 1 surgical intervention (95.1%); 68.4% underwent at least 1 endoscopic intervention. Patients diagnosed with high- vs low-risk UTUC were more likely to undergo nephroureterectomy (83.6% vs 72.0%; P < .001); few patients with low-risk disease were exclusively managed endoscopically (16.9%). At 365 days after diagnosis, costs of care for high- vs low-risk UTUC were statistically significantly higher ($108 520 vs $91 233; median difference $16 704, 95% confidence interval [CI] = $11 619 to $21 778; P < .001). Those with high-risk UTUC had worse cancer-specific and overall survival compared with patients with low-risk UTUC (cancer-specific survival hazard ratio [HR] = 4.14, 95% CI = 3.19 to 5.37; overall survival HR = 1.78, 95% CI = 1.62 to 1.96).

Conclusions

UTUC continues to be managed primarily with nephroureterectomy, regardless of risk stratification, and patients with high-risk UTUC have worse overall and cancer-specific survival. Substantial costs are associated with management of low- and high-risk UTUC, with the latter being more costly up to 1 year from diagnosis.
A case of dermatofibrosarcoma protuberans with neurofibromatous change
Authors: Kudoh Kazuhiro , Itabashi Chieko , Arai Eiichi , Ohshika Shusa , Mizukami Hiroki
Published: September 2021

A 31-year-old man with posterior neck mass visited a hospital. The mass recurred four times on the same location during the past 6 years. Needle biopsy diagnosis was suspicious for benign stromal tumor. Tumor excision was performed 3 months after the biopsy. The tumor size was 8.3 × 4.5 cm and was located at subcutaneous tissue. Histologically, main tumor cells showed comma-shaped nuclei, which are same as neurofibroma. Immunohistochemically, tumor cells were positive for vimentin, CD34, but were negative for S-100. Fluorescence in situ hybridization analysis disclosed a split signal of PDGFB gene. Reverse transcriptase-polymerase chain reaction clarified COL1A1 exon 47/PDGFB exon 2 chimeric gene. Final diagnosis was dermatofibrosarcoma protuberans (DFSP) with neurofibromatous change. DFSP with neurofibromatous change is rare and could be misdiagnosed as benign tumor, especially in a biopsy specimen. Molecular diagnosis is a promising aid in a challenging case and in biopsy specimens.
A rare case of multiple giant colonic diverticula successfully treated with laparoscopic sigmoidectomy
Authors: Merritt Clay M , Xing Chuheng , Schwartz Mary R , Bailey Harold R , Van Eps Jeffrey L
Published: September 2021

Colonic diverticulosis is pervasive in Western society, with over half of individuals over the age of 60 carrying the diagnosis. A Giant Colonic Diverticulum (GCD) is a rare presentation of diverticulosis, involving one or more colonic diverticula that measure 4 cm or greater. Less than 200 reports of GCD have been published in the literature. Almost all GCD patients present with symptoms, with abdominal pain being the most common. Diagnosis is usually made with CT imaging and recommended treatment is segmental colectomy. We present an atypical case of GCD with an asymptomatic presentation, initial diagnosis made during endoscopy and a minimally invasive resection of multiple GCD within the same patient.
The Discourse Marker מ ה ז ה (ma ze) to express Rebuking in Rabbinic Hebrew
Authors: Shemesh-Raiskin Rivka
Published: September 2021

The phrase מ ה ז ה (ma ze) is used in Rabbinic Hebrew to express a speech act of rebuking, for example: ? מהזה, עקיבא (‘What is this, ʿAqiba?’). A review of its occurrences reveals its various characteristics: a) it serves as a rhetorical question to express a rebuking; b) it appears in the spoken language; c) it is used especially by one sage when rebuking another sage; and d), syntactically, it appears at the beginning of the sentence and is followed by an address. It seems that its usage in Rabbinic Hebrew is not a continuation of the usage found in Biblical Hebrew, and that it has not continued into Modern Hebrew. This usage as described and exemplified in this article has apparently not been documented in dictionaries of Rabbinic Hebrew nor in the research literature. I suggest viewing מ ה ז ה Hebrew as a rebuking interactional discourse marker.
The Debate of Menaḥem and Dunash and a Frame-work for Non-Triliteral Hebrew Verbal Morphology
Authors: Dachman Joshua
Published: September 2021

This study presents a new suggestion as to the fundamental disagreement between the morphological theories of Menaḥem b. Saruq and Dunash b. Labraṭ, two tenth-century Hebraists with non-triliteral perspectives of the Hebrew root. A framework detailing the possible analyses of Hebrew verbal morphology without a priori assuming the triliteral perspective is first developed. It is noted that the multiplicity of possible analyses in this framework parallels the ‘Segmentation Problem’ of Romance languages due to thematic vowels. Based on analysis of their treatises it is then argued that Menaḥem generally follows one identified method of analysis, and Dunash another. Finally it is suggested that these different methods of analysis are rooted in two different models of morphology, with Menaḥem holding a morpheme-based model and Dunash holding a word-based model. An English translation of a lengthy relevant section of the introduction to Menaḥem’s treatise is given as an appendix.
The Faifi Arabic [St] Reflex of Ṣād: Proto-Semitic or Substrate?
Authors: Davis Stuart , Alfaifi Abdullah
Published: September 2021

This paper argues against the view that the unusual reflex of ṣād as [st] in Faifi Arabic stems from a metathesized version of the Proto-Semitic glottalized affricate * cʾ([tsʾ]), as in Alfaifi and Behnstedt (2010: 53–4), where [st] is assumed to pattern as monosegmental. Instead we propose that the [st] reflex of ṣād in Faifi Arabic reflects a South Arabian ejective or glottalized fricative *sʾ as a substrate feature. We first argue that Faifi Arabic [st] patterns as bisegmental based on linguistic argumentation internal to the dialect. We then discuss *s’as a feature of South Arabian varieties that can be considered as part of the Faifi substrate. We then detail how it is phonetically plausible for ejective sʾ to ‘break’ into a sequence of a fricative followed by a stop, such as [st], accounting for its bisegmental patterning and its realization as pharyngealized [ṣ] where [st] is phonotactically impossible.
CsMYB96 confers resistance to water loss in citrus fruit by simultaneous regulation of water transport and wax biosynthesis
Authors: Zhang Mingfei , Wang Jinqiu , Liu Ruilian , Liu Hai , Yang Hongbin , Zhu Zhifeng , Xu Rangwei , Wang Pengwei , Deng Xiuxin , Xue Shaowu , Zhu Feng , Cheng Yunjiang
Published: September 2021

A Citrus sinensis R2R3 MYB transcription factor (CsMYB96) has previously been shown to be strongly associated with the expression of many genes related to wax biosynthesis in the fruit. In this study, CsMYB96 was found to alleviate water loss by simultaneously regulating the expression of genes encoding plasma membrane intrinsic proteins (CsPIPs) and wax-related genes. Expression profiling indicated that CsPIP1;1 and CsPIP2;4 had high expression that was representative of other aquaporins, and they were down-regulated in the peel of post-harvest citrus fruit. CsPIP2;4 was further characterized as the predominant CsPIP, with high expression and high-water channel activity. Transient overexpression of CsPIP2;4 accelerated water loss in citrus fruit. In silico analysis further indicated that the expression of CsMYB96 had a significant negative correlation with that of CsPIPs. In vivo and in vitro experiments confirmed that CsMYB96 was able to directly repress the expression of CsPIPs. In addition, CsMYB96 was able to activate wax-related genes and promote wax biosynthesis for defense against water loss. Transient and stable overexpression of CsMYB96 reduced water loss from both citrus fruit and Arabidopsis.
Interactions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass (Panicum virgatum L.)
Authors: Griffiths Marcus , Wang Xueyan , Dhakal Kundan , Guo Haichao , Seethepalli Anand , Kang Yun , York Larry M
Published: September 2021

The response of plant growth and development to nutrient and water availability is an important adaptation for abiotic stress tolerance. Roots need to intercept both passing nutrients and water while foraging into new soil layers for further resources. Substantial amounts of nitrate can be lost in the field when leaching into groundwater, yet very little is known about how deep rooting affects this process. Here, we phenotyped root system traits and deep 15N nitrate capture across 1.5 m vertical profiles of solid media using tall mesocosms in switchgrass (Panicum virgatum L.), a promising cellulosic bioenergy feedstock. Root and shoot biomass traits, photosynthesis and respiration measures, and nutrient uptake and accumulation traits were quantified in response to a water and nitrate stress factorial experiment for switchgrass upland (VS16) and lowland (AP13) ecotypes. The two switchgrass ecotypes shared common plastic abiotic responses to nitrogen (N) and water availability, and yet had substantial genotypic variation for root and shoot traits. A significant interaction between N and water stress combination treatments for axial and lateral root traits represents a complex and shared root development strategy for stress mitigation. Deep root growth and 15N capture were found to be closely linked to aboveground growth. Together, these results represent the wide genetic pool of switchgrass and show that deep rooting promotes nitrate capture, plant productivity, and sustainability.
Eight-carbon volatiles: prominent fungal and plant interaction compounds
Authors: Pennerman Kayla K , Yin Guohua , Bennett Joan W
Published: September 2021

Signaling via volatile organic compounds (VOCs) has historically been studied mostly by entomologists; however, botanists and mycologists are increasingly aware of the physiological potential of chemical communication in the gas phase. Most research to date focuses on the observed effects of VOCs on different organisms such as differential growth or metabolite production. However, with the increased interest in volatile signaling, more researchers are investigating the molecular mechanisms for these effects. Eight-carbon VOCs are among the most prevalent and best-studied fungal volatiles. Therefore, this review emphasizes examples of eight-carbon VOCs affecting plants and fungi. These compounds display different effects that include growth suppression in both plants and fungi, induction of defensive behaviors such as accumulation of mycotoxins, phytohormone signaling cascades, and the inhibition of spore and seed germination. Application of ‘-omics’ and other next-generation sequencing techniques is poised to decipher the mechanistic basis of volatiles in plant–fungal communication.
Efficacy of POC Antibody Assays after COVID-19 Infection and Potential Utility for “Immunity Passports”
Authors: Shalaby Akram , Laharwani Hansini , Bates John T , Kyle Patrick B
Published: September 2021

Objective

Numerous manufacturers market lateral flow assays for the detection of SARS-CoV-2 antibodies, but there are many questions about the reliability and efficacy of these tests.

Materials and Methods

Serum specimens from 60 individuals were analyzed using 2 lateral flow antibody assays, an in-house enzyme-linked immunosorbent assay (ELISA), and the Abbott SARS-CoV-2 IgG chemiluminescent immunoassay.

Results

The BioMedomics and Premier Biotech lateral flow assays were positive for IgM in 73.3% and 70% and for IgG in 80% and 73.3% of specimens, respectively. The ELISA assay was positive for IgM and IgG in 73.3% and 86.7% of specimens from infected individuals, whereas the Abbott assay was positive in 80%. The specificities of the 4 assays ranged from 96.7% to 100% for IgM and from 93.3% to 100% for IgG.

Conclusion

Results of the 2 lateral flow assays were comparable to those of the ELISA and Abbott assays. Assay efficacy depended on length of time after SARS-CoV-2 infection.
medusa: Minkowski functionals estimated from Delaunay tessellations of the three-dimensional large-scale structure
Authors: Lippich Martha , Sánchez Ariel G
Published: September 2021

Minkowski functionals (MFs) are a set of statistics that characterize the geometry and topology of the cosmic density field and contain complementary information to the standard two-point analyses. We present medusa, an implementation of an accurate method for estimating the MFs of three-dimensional point distributions. These estimates are inferred from triangulated isodensity surfaces that are constructed from the Delaunay tessellation of the input point sample. medusa can account for periodic boundary conditions, which is crucial for the analysis of N-body simulations. We validate our code against several test samples with known MFs, including Gaussian random fields with a ΛCDM power spectrum, and find excellent agreement with the theory predictions. We use medusa to measure the MFs of synthetic galaxy catalogues constructed from N-body simulations. Our results show clearly non-Gaussian signatures that arise from the non-linear gravitational evolution of the density field. We find that, although redshift-space distortions change our MFs estimates, their impact is considerably reduced if these measurements are expressed as a function of the volume-filling fraction. We also show that the effect of Alcock–Paczynski (AP) distortions on the MFs can be described by scaling them with different powers of the isotropic AP parameter q defined in terms of the volume-averaged distance DV(z). Thus the MFs estimates by medusa are useful probes of non-linearities in the density field, and the expansion and growth of structure histories of the Universe.
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
Authors: Cantalapiedra Carlos P , Hernández-Plaza Ana , Letunic Ivica , Bork Peer , Huerta-Cepas Jaime
Published: September 2021

Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.
Oncogenic KRAS drives radioresistance through upregulation of NRF2-53BP1-mediated non-homologous end-joining repair
Authors: Yang Linlin , Shen Changxian , Estrada-Bernal Adriana , Robb Ryan , Chatterjee Moumita , Sebastian Nikhil , Webb Amy , Mo Xiaokui , Chen Wei , Krishnan Sunil , Williams Terence M
Published: September 2021

KRAS-activating mutations are oncogenic drivers and are correlated with radioresistance of multiple cancers, including colorectal cancer, but the underlying precise molecular mechanisms remain elusive. Herein we model the radiosensitivity of isogenic HCT116 and SW48 colorectal cancer cell lines bearing wild-type or various mutant KRAS isoforms. We demonstrate that KRAS mutations indeed lead to radioresistance accompanied by reduced radiotherapy-induced mitotic catastrophe and an accelerated release from G2/M arrest. Moreover, KRAS mutations result in increased DNA damage response and upregulation of 53BP1 with associated increased non-homologous end-joining (NHEJ) repair. Remarkably, KRAS mutations lead to activation of NRF2 antioxidant signaling to increase 53BP1 gene transcription. Furthermore, genetic silencing or pharmacological inhibition of KRAS, NRF2 or 53BP1 attenuates KRAS mutation-induced radioresistance, especially in G1 phase cells. These findings reveal an important role for a KRAS-induced NRF2-53BP1 axis in the DNA repair and survival of KRAS-mutant tumor cells after radiotherapy, and indicate that targeting NRF2, 53BP1 or NHEJ may represent novel strategies to selectively abrogate KRAS mutation-mediated radioresistance.
SomaMutDB: a database of somatic mutations in normal human tissues
Authors: Sun Shixiang , Wang Yujue , Maslov Alexander Y , Dong Xiao , Vijg Jan
Published: September 2021

De novo mutations, a consequence of errors in DNA repair or replication, have been reported to accumulate with age in normal tissues of humans and model organisms. This accumulation during development and aging has been implicated as a causal factor in aging and age-related pathology, including but not limited to cancer. Due to their generally very low abundance mutations have been difficult to detect in normal tissues. Only with recent advances in DNA sequencing of single-cells, clonal lineages or ultra-high-depth sequencing of small tissue biopsies, somatic mutation frequencies and spectra have been unveiled in several tissue types. The rapid accumulation of such data prompted us to develop a platform called SomaMutDB (https://vijglab.einsteinmed.org/SomaMutDB) to catalog the 2.42 million single nucleotide variations (SNVs) and 0.12 million small insertions and deletions (INDELs) thus far identified using these advanced methods in nineteen human tissues or cell types as a function of age or environmental stress conditions. SomaMutDB employs a user-friendly interface to display and query somatic mutations with their functional annotations. Moreover, the database provides six powerful tools for analyzing mutational signatures associated with the data. We believe such an integrated resource will prove valuable for understanding somatic mutations and their possible role in human aging and age-related diseases.
scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse
Authors: Yang Xiaoxiao , Tong Yang , Liu Gerui , Yuan Jiapei , Yang Yang
Published: September 2021

Alternative polyadenylation (APA) has been widely recognized as a crucial step during the post-transcriptional regulation of eukaryotic genes. Recent studies have demonstrated that APA exerts key regulatory roles in many biological processes and often occurs in a tissue- and cell-type-specific manner. However, to our knowledge, there is no database incorporating information about APA at the cell-type level. Single-cell RNA-seq is a rapidly evolving and powerful tool that enable APA analysis at the cell-type level. Here, we present a comprehensive resource, scAPAatlas (http://www.bioailab.com:3838/scAPAatlas), for exploring APA across different cell types, and interpreting potential biological functions. Based on the curated scRNA-seq data from 24 human and 25 mouse normal tissues, we systematically identified cell-type-specific APA events for different cell types and examined the correlations between APA and gene expression level. We also estimated the crosstalk between cell-type-specific APA events and microRNAs or RNA-binding proteins. A user-friendly web interface has been constructed to support browsing, searching and visualizing multi-layer information of cell-type-specific APA events. Overall, scAPAatlas, incorporating a rich resource for exploration of APA at the cell-type level, will greatly help researchers chart cell type with APA and elucidate the biological functions of APA.
VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes
Authors: Sun Qinglan , Shu Chang , Shi Wenyu , Luo Yingfeng , Fan Guomei , Nie Jingyi , Bi Yuhai , Wang Qihui , Qi Jianxun , Lu Jian , Zhou Yuanchun , Shen Zhihong , Meng Zhen , Zhang Xinjiao , Yu Zhengfei , Gao Shenghan , Wu Linhuan , Ma Juncai , Hu Songnian
Published: September 2021

The genomic variations of SARS-CoV-2 continue to emerge and spread worldwide. Some mutant strains show increased transmissibility and virulence, which may cause reduced protection provided by vaccines. Thus, it is necessary to continuously monitor and analyze the genomic variations of SARS-COV-2 genomes. We established an evaluation and prewarning system, SARS-CoV-2 variations evaluation and prewarning system (VarEPS), including known and virtual mutations of SARS-CoV-2 genomes to achieve rapid evaluation of the risks posed by mutant strains. From the perspective of genomics and structural biology, the database comprehensively analyzes the effects of known variations and virtual variations on physicochemical properties, translation efficiency, secondary structure, and binding capacity of ACE2 and neutralizing antibodies. An AI-based algorithm was used to verify the effectiveness of these genomics and structural biology characteristic quantities for risk prediction. This classifier could be further used to group viral strains by their transmissibility and affinity to neutralizing antibodies. This unique resource makes it possible to quickly evaluate the variation risks of key sites, and guide the research and development of vaccines and drugs. The database is freely accessible at www.nmdc.cn/ncovn.