bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and phenotypic profiling of colorectal cancer patients in West Africa reveals biological insights
Authors: Alatise Olusegun Isaac , Knapp Gregory C. , Sharma Avinash , Chatila Walid K. , Arowolo Olukayode A. , Olasehinde Olalekan , Famurewa Olusola C. , Omisore Adeleye D. , Komolafe Akinwumi O. , Olaofe Olaejinrinde O. , Katung Aba I. , Ibikunle David E. , Egberongbe Adedeji A. , Olatoke Samuel A. , Agodirin Sulaiman O. , Adesiyun Olusola A. , Adeyeye Ademola , Kolawole Oladapo A. , Olakanmi Akinwumi O. , Arora Kanika , Constable Jeremy , Shah Ronak , Basunia Azfar , Sylvester Brooke , Wu Chao , Weiser Martin R. , Seier Ken , Gonen Mithat , Stadler Zsofia K. , Kemel Yelena , Vakiani Efsevia , Berger Michael F. , Chan Timothy A. , Solit David B. , Shia Jinru , Sanchez-Vega Francisco , Schultz Nikolaus , Brennan Murray , Smith J. Joshua , Kingham T. Peter 
Published: November 2021

AbstractUnderstanding the molecular and phenotypic profile of colorectal cancer (CRC) in West Africa is vital to addressing the regions rising burden of disease. Tissue from unselected Nigerian patients was analyzed with a multigene, next-generation sequencing assay. The rate of microsatellite instability is significantly higher among Nigerian CRC patients (28.1%) than patients from The Cancer Genome Atlas (TCGA, 14.2%) and Memorial Sloan Kettering Cancer Center (MSKCC, 8.5%,P < 0.001). In microsatellite-stable cases, tumors from Nigerian patients are less likely to haveAPCmutations (39.1% vs. 76.0% MSKCCP < 0.001) and WNT pathway alterations (47.8% vs. 81.9% MSKCC,P < 0.001); whereas RAS pathway alteration is more prevalent (76.1% vs. 59.6%,P = 0.03). Nigerian CRC patients are also younger and more likely to present with rectal disease (50.8% vs. 33.7% MSKCC,P < 0.001). The findings suggest a unique biology of CRC in Nigeria, which emphasizes the need for regional data to guide diagnostic and treatment approaches for patients in West Africa.
Trpm5 channels encode bistability of spinal motoneurons and ensure motor control of hindlimbs in mice
Authors: Bos Rémi , Drouillas Benoît , Bouhadfane Mouloud , Pecchi Emilie , Trouplin Virginie , Korogod Sergiy M. , Brocard Frédéric 
Published: November 2021

AbstractBistable motoneurons of the spinal cord exhibit warmth-activated plateau potential driven by Na+ and triggered by a brief excitation. The thermoregulating molecular mechanisms of bistability and their role in motor functions remain unknown. Here, we identify thermosensitive Na+-permeable Trpm5 channels as the main molecular players for bistability in mouse motoneurons. Pharmacological, genetic or computational inhibition of Trpm5 occlude bistable-related properties (slow afterdepolarization, windup, plateau potentials) and reduce spinal locomotor outputs while central pattern generators for locomotion operate normally. At cellular level, Trpm5 is activated by a ryanodine-mediated Ca2+ release and turned off by Ca2+ reuptake through the sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) pump. Mice in which Trpm5 is genetically silenced in most lumbar motoneurons develop hindlimb paresis and show difficulties in executing high-demanding locomotor tasks. Overall, by encoding bistability in motoneurons, Trpm5 appears indispensable for producing a postural tone in hindlimbs and amplifying the locomotor output.
Chromatin network retards nucleoli coalescence
Authors: Qi Yifeng , Zhang Bin 
Published: November 2021

AbstractNuclear bodies are membraneless condensates that may form via liquid-liquid phase separation. The viscoelastic chromatin network could impact their stability and may hold the key for understanding experimental observations that defy predictions of classical theories. However, quantitative studies on the role of the chromatin network in phase separation have remained challenging. Using a diploid human genome model parameterized with chromosome conformation capture (Hi-C) data, we study the thermodynamics and kinetics of nucleoli formation. Dynamical simulations predict the formation of multiple droplets for nucleolar particles that experience specific interactions with nucleolus-associated domains (NADs). Coarsening dynamics, surface tension, and coalescence kinetics of the simulated droplets are all in quantitative agreement with experimental measurements for nucleoli. Free energy calculations further support that a two-droplet state, often observed for nucleoli in somatic cells, is metastable and separated from the single-droplet state with an entropic barrier. Our study suggests that nucleoli-chromatin interactions facilitate droplets’ nucleation but hinder their coarsening due to the coupled motion between droplets and the chromatin network: as droplets coalesce, the chromatin network becomes increasingly constrained. Therefore, the chromatin network supports a nucleation and arrest mechanism to stabilize the multi-droplet state for nucleoli and possibly for other nuclear bodies.
Theory of branching morphogenesis by local interactions and global guidance
Authors: Uçar Mehmet Can , Kamenev Dmitrii , Sunadome Kazunori , Fachet Dominik , Lallemend Francois , Adameyko Igor , Hadjab Saida , Hannezo Edouard 
Published: November 2021

AbstractBranching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales.
SARS-CoV-2 virus transfers to skin through contact with contaminated solids
Authors: Behzadinasab Saeed , Chin Alex W. H. , Hosseini Mohsen , Poon Leo L. M. , Ducker William A. 
Published: November 2021

AbstractTransfer of SARS-CoV-2 from solids to fingers is one step in infection via contaminated solids, and the possibility of infection from this route has driven calls for increased frequency of handwashing during the COVID-19 pandemic. To analyze this route of infection, we measured the percentage of SARS-CoV-2 that was transferred from a solid to an artificial finger. A droplet of SARS-CoV-2 suspension (1 µL) was placed on a solid, and then artificial skin was briefly pressed against the solid with a light force (3 N). Transfer from a variety of solids was detected, and transfer from the non-porous solids, glass, stainless steel, and Teflon, was substantial when the droplet was still wet. The viral titer for the finger was 13–16% or 0.8–0.9 log less than for the input droplet. Transfer still occurred after the droplet evaporated, but was smaller, 3–9%. We found a lower level of transfer from porous solids but did not find a significant effect of solid wettability for non-porous solids.
Synthesis of low sidelobe level antenna arrays through only main lobe assumption
Authors: Khalaj-Amirhosseini Mohammad 
Published: November 2021

AbstractAn analytic method is proposed to design uniformly spaced arrays so that have as low as possible sidelobe level and having directivity as close as to that of uniformly excited arrays. The ideal array factor of arrays is assumed to have only one main lobe. The actual synthesized array would have sidelobe levels which can be controlled by a parameter. Some examples are given to verify the effectiveness of the presented method.
General intelligence disentangled via a generality metric for natural and artificial intelligence
Authors: Hernández-Orallo José , Loe Bao Sheng , Cheke Lucy , Martínez-Plumed Fernando , Ó hÉigeartaigh Seán 
Published: November 2021

AbstractSuccess in all sorts of situations is the most classical interpretation of general intelligence. Under limited resources, however, the capability of an agent must necessarily be limited too, and generality needs to be understood as comprehensive performance up to a level of difficulty. The degree of generality then refers to the way an agent’s capability is distributed as a function of task difficulty. This dissects the notion of general intelligence into two non-populational measures, generality and capability, which we apply to individuals and groups of humans, other animals and AI systems, on several cognitive and perceptual tests. Our results indicate that generality and capability can decouple at the individual level: very specialised agents can show high capability and vice versa. The metrics also decouple at the population level, and we rarely see diminishing returns in generality for those groups of high capability. We relate the individual measure of generality to traditional notions of general intelligence and cognitive efficiency in humans, collectives, non-human animals and machines. The choice of the difficulty function now plays a prominent role in this new conception of generality, which brings a quantitative tool for shedding light on long-standing questions about the evolution of general intelligence and the evaluation of progress in Artificial General Intelligence.
PERG adaptation for detection of retinal ganglion cell dysfunction in glaucoma: a pilot diagnostic accuracy study
Authors: Salgarello T. , Cozzupoli G. M. , Giudiceandrea A. , Fadda A. , Placidi G. , De Siena E. , Amore F. , Rizzo S. , Falsini B. 
Published: November 2021

AbstractIt has been previously demonstrated that the adaptive phase changes of steady-state pattern electroretinogram (SS-PERG), recorded during 4-min presentation of patterned stimuli, are reduced in glaucoma suspects and patients compared to normal subjects. Our study aims at testing the hypothesis that adaptive changes of SS-PERG, recorded using the novel optimized Next Generation PERG (PERGx) protocol, differ between glaucoma patients and controls. In this pilot cross-sectional study, we included 28 glaucoma patients and 17 age-matched normal subjects. Both patients and controls underwent a full ophthalmologic examination, visual field testing, OCT and PERGx. The PERGx signal was sampled over 2 min (providing 1 noise and 9 signal packets) in response to alternating gratings generated on an OLED display. PERGx amplitude and phase were analyzed to quantify adaptive changes over recording time. Receiver operating characteristic (ROC) curves were used to study the diagnostic accuracy of PERGx parameters in distinguishing glaucoma patients from normal subjects. PERGx amplitude and phase data showed declining trends in both groups. PERGx amplitude slope and grand-average vector amplitude and phase were significantly different in patients compared to controls (p < 0.01), whereas phase angular dispersion was greater in patients but not significantly different between the two groups. The area under the ROC curves were 0.87 and 0.76 for PERGx amplitude slope and grand-average vector amplitude, and 0.62 and 0.87 for PERGx angular dispersion and grand-average vector phase, respectively. The PERGx paradigm resulted highly accurate in detecting the reduction of amplitude adaptive changes in glaucoma patients, presumably due to the loss of functional retinal ganglion cell autoregulation. Thus, PERG adaptation, recorded by this new protocol, might be helpful in the identification and diagnosis of early glaucomatous dysfunction.
Breeding for higher yield, early maturity, wider adaptability and waterlogging tolerance in soybean (Glycine max L.): A case study
Authors: Maranna Shivakumar , Nataraj Vennampally , Kumawat Giriraj , Chandra Subhash , Rajesh Vangala , Ramteke Rajkumar , Patel Ram Manohar , Ratnaparkhe Milind B. , Husain S. M. , Gupta Sanjay , Khandekar Nita 
Published: November 2021

AbstractBreeding for higher yield and wider adaptability are major objectives of soybean crop improvement. In the present study, 68 advanced breeding lines along with seven best checks were evaluated for yield and attributing traits by following group balanced block design. Three blocks were constituted based on the maturity duration of the breeding lines. High genetic variability for the twelve quantitative traits was found within and across the three blocks. Several genotypes were found to outperform check varieties for yield and attributing traits. During the same crop season, one of the promising entries, NRC 128,was evaluated across seven locations for its wider adaptability and it has shown stable performance in Northern plain Zone with > 20% higher yield superiority over best check PS 1347. However, it produced 9.8% yield superiority over best check in Eastern Zone. Screening for waterlogging tolerance under artificial conditions revealed that NRC 128 was on par with the tolerant variety JS 97–52. Based on the yield superiority, wider adaptability and waterlogging tolerance, NRC 128 was released and notified by Central Varietal Release Committee (CVRC) of India, for its cultivation across Eastern and Northern Plain Zones of India.
Pleistocene allopatric differentiation followed by recent range expansion explains the distribution and molecular diversity of two congeneric crustacean species in the Palaearctic
Authors: Lukić Dunja , Pinceel Tom , Marrone Federico , Mioduchowska Monika , Vad Csaba F. , Brendonck Luc , Ptacnik Robert , Horváth Zsófia 
Published: November 2021

AbstractPleistocene glaciations had a tremendous impact on the biota across the Palaearctic, resulting in strong phylogeographic signals of range contraction and rapid postglacial recolonization of the deglaciated areas. Here, we explore the diversity patterns and history of two sibling species of passively dispersing taxa typical of temporary ponds, fairy shrimps (Anostraca). We combine mitochondrial (COI) and nuclear (ITS2 and 18S) markers to conduct a range-wide phylogeographic study including 56 populations ofBranchinecta feroxandBranchinecta orientalisin the Palaearctic. Specifically, we investigate whether their largely overlapping ranges in Europe resulted from allopatric differentiation in separate glacial refugia followed by a secondary contact and reconstruct their postglacial recolonization from the inhabited refugia. Our results suggest the existence of distinct refugia for the two species, with genetic divergence among intraspecific lineages consistent with late Pleistocene glacial cycles. WhileB. feroxlineages originated from Mediterranean refugia, the origin ofB. orientalislineages was possibly located on the Pannonian Plain. We showed that most dispersal events predominantly happened within 100 km, coupled with several recent long-distance events (> 1000 km). Hence the regional habitat density of suitable habitats in Central Europe is possibly a key to the co-existence of the two species. Overall, our study illustrates how isolation in combination with stochastic effects linked to glacial periods are important drivers of the allopatric differentiation of Palaearctic taxa.
Diagnostic performance of rapid antigen tests (RATs) for SARS-CoV-2 and their efficacy in monitoring the infectiousness of COVID-19 patients
Authors: Routsias John G. , Mavrouli Maria , Tsoplou Panagiota , Dioikitopoulou Kyriaki , Tsakris Athanasios 
Published: November 2021

AbstractThe most widely used test for the diagnosis of SARS-CoV-2 infection is a PCR test. PCR has very high sensitivity and is able to detect very low amounts of RNA. However, many individuals receiving a positive test result in a context of a PCR-based surveillance might be infected with SARS-CoV-2, but they are not contagious at the time of the test. The question arises regards if the cost effective, portable rapid antigen tests (RATs) have a better performance than PCR in identification of infectious individuals. In this direction, we examined the diagnostic performance of RATs from 14 different manufacturers in 400 clinical samples with known rRT-PCR cycles threshold (cT) and 50 control samples. Substantial variability was observed in the limit of detection (LOD) of different RATs (cT = 26.8–34.7). The fluorescence-based RAT exhibited a LOD of cT = 34.7. The use of the most effective RATs leads to true positive rates (sensitivities) of 99.1% and 90.9% for samples with cT ≤ 30 and cT ≤ 33, respectively, percentages that can guarantee a sensitivity high enough to identify contagious patients. RAT testing may also substantially reduce the quarantine period for infected individuals without compromising personal or public safety.
The network limits of infectious disease control via occupation-based targeting
Authors: Avraam Demetris , Obradovich Nick , Pescetelli Niccolò , Cebrian Manuel , Rutherford Alex 
Published: November 2021

AbstractPolicymakers commonly employ non-pharmaceutical interventions to reduce the scale and severity of pandemics. Of non-pharmaceutical interventions, physical distancing policies—designed to reduce person-to-person pathogenic spread – have risen to recent prominence. In particular, stay-at-home policies of the sort widely implemented around the globe in response to the COVID-19 pandemic have proven to be markedly effective at slowing pandemic growth. However, such blunt policy instruments, while effective, produce numerous unintended consequences, including potentially dramatic reductions in economic productivity. In this study, we develop methods to investigate the potential to simultaneously contain pandemic spread while also minimizing economic disruptions. We do so by incorporating both occupational and contact network information contained within an urban environment, information that is commonly excluded from typical pandemic control policy design. The results of our methods suggest that large gains in both economic productivity and pandemic control might be had by the incorporation and consideration of simple-to-measure characteristics of the occupational contact network. We find evidence that more sophisticated, and more privacy invasive, measures of this network do not drastically increase performance.
Efficacy of shear wave elasticity for evaluating myocardial hypertrophy in hypertensive rats
Authors: Takaya Yoichi , Nakamura Kazufumi , Nakayama Rie , Ohtsuka Hiroaki , Amioka Naofumi , Kondo Megumi , Akazawa Kaoru , Ohno Yuko , Ichikawa Keishi , Saito Yukihiro , Akagi Satoshi , Yoshida Masashi , Miyoshi Toru , Ito Hiroshi 
Published: November 2021

AbstractShear wave (SW) imaging is a novel ultrasound-based technique for assessing tissue characteristics. SW elasticity may be useful to assess the severity of hypertensive left ventricular (LV) hypertrophy. This study aimed to evaluate the efficacy of SW elasticity for assessing the degree of myocardial hypertrophy using hypertensive rats. Rats were divided into hypertension group and control group. SW elasticity was measured on the excised heart. Myocardial hypertrophy was assessed histologically. LV weight was greater in hypertension group. An increase in interventricular septum and LV free wall thicknesses was observed in hypertension group. SW elasticity was significantly higher in hypertension group than in control group (14.6 ± 4.3 kPa vs. 6.5 ± 1.1 kPa, P < 0.01). The cross-sectional area of cardiomyocytes was larger in hypertension group than in control group (397 ± 50 μm2 vs. 243 ± 14 μm2, P < 0.01), and SW elasticity was positively correlated with the cross-sectional area of cardiomyocytes (R = 0.96, P < 0.01). This study showed that SW elasticity was higher in hypertensive rats and was closely correlated with the degree of myocardial hypertrophy, suggesting the efficacy of SW elasticity for estimating the severity of hypertensive LV hypertrophy.
Camel milk ameliorates inflammatory mechanisms in an alcohol-induced liver injury mouse model
Authors: Ming Liang , Qi Bule , Hao Shiqi , Ji Rimutu 
Published: November 2021

AbstractCamel milk (CM) is considered to protect the liver in the practice of traditional medicine in nomadic areas. The purpose of the present study was to investigate the effects of CM on the hepatic biochemical and multiple omics alterations induced by chronic alcoholic liver disease (ALD). An intragastric gavage mice Lieber DeCarli + Gao binge model (NIAAA model) was employed to investigate the inflammatory mechanism of camel milk on the liver tissue of mice. A gut microbiota of the feces of mice and transcriptomic and proteomic analyses of the liver of mice were performed. Analysis of serum and liver biochemical indexes revealed that camel milk not only prevents alcohol-induced colonic dysfunction and lipid accumulation, but also regulates oxidative stress and inflammatory cytokine production to protect against chronic ALD in mouse. The gut microbial community of mice treated with camel milk was more similar to the untreated control group than to the model group, indicating that the intake of camel milk pre- and post-alcohol gavage effectively prevents and alleviates the intestinal microbial disorder caused by chronic alcoholism in mice. Furthermore, the results of the transcriptomic and proteomic analyses of the liver tissue showed that camel milk can improve alcoholic liver injury in mice by regulating inflammatory factors and immune system disruptions. This study provides insights into the molecular mechanism by which camel milk can be developed as a potential functional food with no side effects and against liver injury.
Incorporation of next-generation sequencing in clinical practice using solid and liquid biopsy for patients with non-Hodgkin’s lymphoma
Authors: Bastos-Oreiro Mariana , Suárez-González Julia , Andrés-Zayas Cristina , Carrión Natalia Carolina , Moreno Solsiré , Carbonell Diego , Chicano María , Muñiz Paula , Sanz Laura , Diaz-Crespo Francisco Javier , Menarguez Javier , Diez-Martín José Luis , Buño Ismael , Martínez-Laperche Carolina 
Published: November 2021

AbstractAlthough next-generation sequencing (NGS) data on lymphomas require further validation before being implemented in daily practice, the clinical application of NGS can be considered right around the corner. The aim of our study was to validate an NGS lymphoid panel for tissue and liquid biopsy with the most common types of non-Hodgkin’s lymphoma [follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL)]. In this series, 372 somatic alterations were detected in 93.6% (44/47) of the patients through tissue biopsy. In FL, we identified 93 somatic alterations, with a median of 7.4 mutations per sample. In DLBCL, we detected 279 somatic variants with a median of 8.6 mutations (range 0–35). In 92% (24/26) of the cases, we were able to detect some variant in the circulating tumor DNA. We detected a total of 386 variants; 63.7% were detected in both types of samples, 13.2% were detected only in the circulating tumor DNA, and 23% were detected only in the tissue biopsy. We found a correlation between the number of circulating tumor DNA mutations, advanced stage, and bulky disease. The genetic alterations detected in this panel were consistent with those previously described at diagnosis. The liquid biopsy sample is therefore a complementary tool that can provide new genetic information, even in cases where a solid biopsy cannot be performed or an insufficient sample was obtained. In summary, we describe and analyze in this study the findings and difficulties encountered when incorporating liquid biopsy into clinical practice in non-Hodgkin’s lymphoma at diagnosis.