bluuebunny/crossref_metadata_2025 huggingface dataset:
Momentum transfer driven by fluctuations in relativistic counter-propagating electron beams
Authors: Ghizzo A , Del Sarto D
Published: February 2021

A semi-Lagrangian relativistic Vlasov–Maxwell solver is used to describe the non-linear momentum transfer between electron beams, which is driven by spontaneous fluctuations in the oblique filamentation instability (a type of Weibel mode) in two-dimensional plasmas. For counter-streaming plasmas, these filamentation instabilities may strengthen the generation of a fine structure of the distribution function in phase space. Properties of such counter-streaming beams are investigated using full-kinetic simulations and a Hamiltonian reduction technique based on the invariance of the transverse canonical momentum, the so-called multi-stream model. In the regime where

k

d

e

≫
1

,

k

being the wavevector and d

e
the electron skin depth, a momentum transfer takes place when a mesoscale current filamentation mode couples with microscopic phase-space fluctuations. This regime is characterized by the appearance of filamentation modes with large wavenumbers and large amplitude fluctuations, which induce variations of the L
2-norm of the plasma in link with the self-organization of counter-streaming electron beams. We also discuss some theoretical aspects of information theory that highlight the role of the (reversible) entropy production in momentum transfer, thus by clarifying the connections between (microscopic) fluctuations of the distribution function and the fundamental aspects of the filamentation in Vlasov theory. The momentum transfer between beams is quantitatively analyzed by means of both theoretical estimations and numerical experiments.
Scattering in the Ising model with the quantum Lanczos algorithm
*
Authors: Yeter-Aydeniz Kübra , Siopsis George , Pooser Raphael C
Published: February 2021

Time evolution and scattering simulation in phenomenological models are of great interest for testing and validating the potential for near-term quantum computers to simulate quantum field theories. Here, we simulate one-particle propagation and two-particle scattering in the one-dimensional transverse Ising model for 3 and 4 spatial sites with periodic boundary conditions on a quantum computer. We use the quantum Lanczos algorithm to obtain all energy levels and corresponding eigenstates of the system. We simplify the quantum computation by taking advantage of the symmetries of the system. These results enable us to compute one- and two-particle transition amplitudes, particle numbers for spatial sites, and the transverse magnetization as functions of time. The quantum circuits were executed on various IBM Q superconducting hardware. The experimental results are in very good agreement with the values obtained using exact diagonalization.
Creep properties and microstructure of a Mg-6Al-1Nd-1.5Gd alloy at temperatures above 150 °C
Authors: Wang Wuxiao , Liu Jian , Wang Na , Qin Zihe , Qin Shaoyong , Guan Shuwen
Published: February 2021

Compressive creep behavior of a Mg-Al alloy containing a small amount of Nd and Gd (Mg-6Al-1Nd-1.5Gd) was investigated at temperatures from 150 °C to 200 °C under a constant applied stress of 90 MPa, and its microstructure before and after creep testing was compared. Results showed that steady-state creep rate of the alloy was only 1.946 × 10−8 /s at 150 °C, and was increased by four times and almost one order of magnitude at 175 °C and 200 °C, respectively. The microstructure of the alloy mainly consists of α-Mg, β-Mg17Al12 phases, and Al2RE phases, which were distributed both in dendrites of α-Mg and at grain boundaries originally. After creep for 120 h, more Al2RE phases were aggregated at grain boundaries. The continuous β-Mg17Al12 phase turned into dispersed dot-like or blocky particles. As the test temperature increased, the number of dislocation lines gradually increased due to the increase of creep strain. Meanwhile, dislocation tangle and dislocation pile-ups occurred near grain boundaries. However, obvious slip traces and slip lines appeared inside α-Mg dendrites at 175 °C and 200 °C, respectively, indicating that 〈c + a〉 non-basal slip system was activated, creep resistance decreased dramatically.
Diagnostic software proposal for bone scan follow-up using false color based on the gammagrams analysis from gray tone histograms
Authors: Jaramillo Núñez Alberto , Arriaga Hernández Jesús Alonso , Cuevas Otahola Bolivia , Pérez Meza Mónica , Sánchez Rinza Bárbara
Published: February 2021

In this work we introduce a technique to speed up the interpretation of bone scans with the aim of determining the presence or absence of metastatic disease. We use gray tone histograms, resembling the use of band-pass filters, in order to ensure a reliable interpretation of the bone scan, therefore providing an accurate diagnosis. We draw particular attention to three cases. The first case corresponds to shifted histograms. If the histogram is shifted toward the origin, the bone scan is free of metastasis. If it is shifted to the right and slightly broadened, this indicates the presence of a bone scan anomaly other than metastasis. On the other hand, if the histogram is broadened and shifted to the left, this suggests the presence of metastatic disease. The second case corresponds to a histogram with noticeable fluctuations, indicating the presence of metastasis. Such fluctuations could become local maxima peaks, indicating the advance of the metastasis. The third case corresponds to the false color results, displayed in terms of the gray tones, observed in the histogram. Such false color is assigned from the construction of a 7-color palette and is selected in terms of the gray tones range. This eases the ad hoc false color assignation for visualization purposes. The final diagnosis is carried out in terms of the color, geometry, extension, and location of the region of interest in the images. Our proposed technique has the potential to be used in high-demand oncology centers due to its simplicity and diagnostic efficiency, confirmed and tested by specialists in the Centro Medico Siglo XXI (XXI Century Medical Center), CDMX-México.
Space survivability for printed electronics applications
Authors: Ouchen Fahima , Aga Roberto , Harvey Malia , Heckman Emily
Published: February 2021

The effects of atomic oxygen (AO) in low earth orbit and the physical effects of space launch on printed materials were studied for aerosol-jet printed Au and Ag through a 6 month exposure period on the Materials International Space Station Experiment (MISSE). RF and DC test platforms were designed for two printed electronics-compatible substrates (Rogers CLTE-XT and Ferro L8) to assess the amount of degradation caused by AO exposure in space. A passivation layer of CORIN-XLS applied over the printed metal traces was also studied for its effectiveness. Both bare and passivated test structures of printed Ag and Au traces were exposed to low earth orbit on the 10th MISSE mission. The effects of AO and the 6 month space exposure on the samples are reported here.
Asymmetrical reproductive barriers in sympatric jewelflowers: are floral isolation, genetic incompatibilities and floral trait displacement connected?
Authors: Christie Kyle , Doan Jonathan P , Mcbride Wendy C , Strauss Sharon Y
Published: February 2021

Floral visitors influence reproductive interactions among sympatric plant species, either by facilitating assortative mating and contributing to reproductive isolation, or by promoting heterospecific pollen transfer, potentially leading to reproductive interference or hybridization. We assessed preference and constancy of floral visitors on two co-occurring jewelflowers [Streptanthus breweri and Streptanthus hesperidis (Brassicaceae)] using field arrays, and quantified two floral rewards potentially important to foraging choice – pollen production and nectar sugar concentration – in a greenhouse common garden. Floral visitors made an abundance of conspecific transitions between S. breweri individuals, which thus experienced minimal opportunities for heterospecific pollen transfer from S. hesperidis. In contrast, behavioural isolation for S. hesperidis was essentially absent due to pollinator inconstancy. This pattern emerged across multiple biotic environments and was unrelated to local density dependence. S. breweri populations that were sympatric with S. hesperidis had higher nectar sugar concentrations than their sympatric congeners, as well as allopatric conspecifics. Previous work shows that S. breweri suffers a greater cost to hybridization than S. hesperidis, and here we find that it also shows asymmetrical floral isolation and floral trait displacement in sympatry. These findings suggest that trait divergence may reduce negative reproductive interactions between sympatric but genetically incompatible relatives.
The evolving role of MUC16 (CA125) in the transformation of ovarian cells and the progression of neoplasia
Authors: Giamougiannis Panagiotis , Martin-Hirsch Pierre L , Martin Francis L
Published: February 2021

MUC16 (the cancer antigen CA125) is the most commonly used serum biomarker in epithelial ovarian cancer, with increasing levels reflecting disease progression. It is a transmembrane glycoprotein with multiple isoforms, undergoing significant changes through the metastatic process. Aberrant glycosylation and cleavage with overexpression of a small membrane-bound fragment consist MUC16-related mechanisms that enhance malignant potential. Even MUC16 knockdown can induce an aggressive phenotype but can also increase susceptibility to chemotherapy. Variable MUC16 functions help ovarian cancer cells avoid immune cytotoxicity, survive inside ascites and form metastases. This review provides a comprehensive insight into MUC16 transformations and interactions, with description of activated oncogenic signalling pathways, and adds new elements on the role of its differential glycosylation. By following the journey of the molecule from pre-malignant states to advanced stages of disease it demonstrates its behaviour, in relation to the phenotypic shifts and progression of ovarian cancer. Additionally, it presents proposed differences of MUC16 structure in normal/benign conditions and epithelial ovarian malignancy.
Effective Human Immunodeficiency Virus Molecular Surveillance Requires Identification of Incident Cases of Infection
Authors: Little Susan J , Chen Tom , Wang Rui , Anderson Christy , Pond Sergei Kosakovsky , Nakazawa Masato , Mathews William C , DeGruttola Victor , Smith Davey M
Published: February 2021

Background

Ending the human immunodeficiency virus (HIV) epidemic requires knowledge of key drivers of spread of HIV infection.

Methods

Between 1996 and 2018, 1119 newly and previously diagnosed, therapy-naive persons with HIV (PWH) from San Diego were followed. A genetic distance–based network was inferred using pol sequences, and genetic clusters grew over time through linkage of sequences from newly observed infections. Cox proportional hazards models were used to identify factors associated with the rate of growth. These results were used to predict the impact of a hypothetical intervention targeting PWH with incident infection. Comparison was made to the Centers for Disease Control and Prevention (CDC) Ending the HIV Epidemic (EHE) molecular surveillance strategy, which prioritizes clusters recently linked to all new HIV diagnoses and does not incorporate data on incident infections.

Results

Overall, 219 genetic linkages to incident infections were identified over a median follow-up of 8.8 years. Incident cluster growth was strongly associated with proportion of PWH in the cluster who themselves had incident infection (hazard ratio, 44.09 [95% confidence interval, 17.09–113.78]). The CDC EHE molecular surveillance strategy identified 11 linkages to incident infections a genetic distance threshold of 0.5%, and 24 linkages at 1.5%.

Conclusions

Over the past 2 decades, incident infections drove incident HIV cluster growth in San Diego. The current CDC EHE molecular detection and response strategy would not have identified most transmission events arising from those with incident infection in San Diego. Molecular surveillance that includes detection of incident cases will provide a more effective strategy for EHE.
Doxycycline Versus Azithromycin for the Treatment of Rectal Chlamydia in Men Who Have Sex With Men: A Randomized Controlled Trial
Authors: Dombrowski Julia C , Wierzbicki Michael R , Newman Lori M , Powell Jonathan A , Miller Ashley , Dithmer Dwyn , Soge Olusegun O , Mayer Kenneth H
Published: February 2021

Background

Azithromycin and doxycycline are both recommended treatments for rectal Chlamydia trachomatis (CT) infection, but observational studies suggest that doxycycline may be more effective.

Methods

This randomized, double-blind, placebo-controlled trial compared azithromycin (single 1-g dose) versus doxycycline (100 mg twice daily for 7 days) for the treatment of rectal CT in men who have sex with men (MSM) in Seattle and Boston. Participants were enrolled after a diagnosis of rectal CT in clinical care and underwent repeated collection of rectal swabs for nucleic acid amplification testing (NAAT) at study enrollment and 2 weeks and 4 weeks postenrollment. The primary outcome was microbiologic cure (CT-negative NAAT) at 4 weeks. The complete case (CC) population included participants with a CT-positive NAAT at enrollment and a follow-up NAAT result; the intention-to-treat (ITT) population included all randomized participants.

Results

Among 177 participants enrolled, 135 (76%) met CC population criteria for the 4-week follow-up visit. Thirty-three participants (19%) were excluded because the CT NAAT repeated at enrollment was negative. Microbiologic cure was higher with doxycycline than azithromycin in both the CC population (100% [70 of 70] vs 74% [48 of 65]; absolute difference, 26%; 95% confidence interval [CI], 16–36%; P < .001) and the ITT population (91% [80 of 88] vs 71% [63 of 89]; absolute difference, 20%; 95% CI, 9–31%; P < .001).

Conclusions

A 1-week course of doxycycline was significantly more effective than a single dose of azithromycin for the treatment of rectal CT in MSM.

Clinical Trials Registration

NCT03608774.
Computational investigation of heat energy interaction for a residential building with a normal clay brick and sinicon brick
Authors: Kummitha Obula Reddy , Kumar R Vijay
Published: February 2021

Most of the building energy is mainly contributing to the achievement of thermal comfort. The cooling load on air conditioners will increase with increased heat transfer into the building from the surroundings. The amount of heat transfer into the building mainly depends on building materials used in construction. In this research, an attempt has been made to analyse the self-sufficient homes’ concept by visualizing variation in heat transfer of the building concerning ordinary clay brick and brick with sinicon composition. The temperature distribution of airflow, time lag, decrement factor, and comfort conditions are investigated concerning these materials with computational fluid dynamics. Numerical modeling has been defined by selecting three-dimensional fluid flow governing equations and the k–ε turbulence model. All the fluid flow governing equations have been solved with the finite-volume second-order upwind discretization and SIMPLE algorithm for pressure–velocity coupling. Numerical results have been analysed for both the materials and we identified that the sinicon brick material for the considered wall thickness (9 inches) had registered an increased time lag (∼2 hrs) and a decreased decrement factor (0.05). This research investigation shows that the sinicon-brick wall strongly decreases heat transfer through it compared to the normal-red brick wall. The sinicon brick significantly reduces the air conditioner’s cooling load by decreasing heat energy penetration into the building.
The Introductive Baka/Bāki in Rural Palestinian Arabic
Authors: Shachmon Ori , Marmorstein Michal
Published: February 2021

The article explores the structure and use of the existential verb baka in Rural Palestinian Arabic for the introduction of orientation sections and fragments in narrative discourse. In clause-initial position the existential verb presents a non-inflecting form, either the 3MSG perfect baka or the MSG active participle bāki. We argue that the noninflectability of baka and bāki is indicative of their syntactic detached-ness from the following unit and is explained by their discourse-disjunctive function. We show that the existential baka/bāki serves to introduce both narrative-initial and narrative-embedded orientation. It may initiate utterances containing simple nominals or whole clauses. The distribution of the specific patterns is determined, inter alia, by the genre of the narrative told. Finally, we propose that the preference of the participle bāki over baka in folktales and in less committed instances of personal narratives may be related to the evidential function of the active participle in the dialects under examination.
MicroRNA319a regulates plant resistance to Sclerotinia stem rot
Authors: Dong Weiguo , Ren Wenqing , Wang Xuan , Mao Yanfei , He Yuke
Published: February 2021

MicroRNA319a (miR319a) controls cell division arrest in plant leaves by inhibiting the expression of TCP (TEOSINTE BRANCHED 1/CYCLOIDEA/PCF) family genes. However, it is unclear whether miR319a influences infection by necrotrophic pathogens and host susceptibility. In this study, we revealed that miR319a affects plant resistance to stem rot disease caused by Sclerotinia sclerotiorum. In Brassica rapa plants infected with S. sclerotiorum, miR319a levels increased while the expression levels of several BraTCP genes significantly decreased compared with those of uninfected plants. Overexpression of BraMIR319a in B. rapa increased the susceptibility of the plants to S. sclerotiorum and aggravated stem rot disease, whereas overexpression of BraTCP4-1 promoted plant resistance. RNA sequencing data revealed a potential relationship between miR319a and pathogen-related WRKY genes. Chromatin immunoprecipitation, electrophoretic mobility shift, and reporter transaction assays showed that BraTCP4-1 could bind to the promoters of WRKY75, WRKY70, and WRKY33 and directly activate these pathogen-related genes. Moreover, the expression levels of WRKY75, WRKY70, and WRKY33 in plants overexpressing BraMIR319a decreased significantly, whereas those of plants overexpressing BraTCP4-1 increased significantly, relative to the wild type. These results suggest that miR319a and its target gene BraTCP4 control stem rot resistance through pathways of WRKY genes.
Topic modelling on archive documents from the 1970s: global policies on refugees
Authors: Grant Philip , Sebastian Ratan , Allassonnière-Tang Marc , Cosemans Sara
Published: February 2021

This study conducts a historical analysis of global policies on refugees within typewritten and digitally born documents (c. 55,000 pages) from international and national archives. The data originate from the 1970s and are stored in archives from the UK and US governments, plus the United Nations High Commissioner for Refugees (UNHCR). The overarching theme is to analyse the involvement of the UK, the USA, and the UNHCR in different refugee cases that occurred during the 1970s. To do so, we (1) identify the main topics in each document; (2) investigate the transmission of topics horizontally (between organizations) and vertically (through time); and (3) suggest targeted areas of the document set for further close reading by historians. Standard Optical Character Recognition and object detection are used to extract information from documents and categorize them. Then, natural language processing (NLP) methods like topic modelling and clustering are used to identify topics and the relationships between them across time. The results identify several main themes covered by different organizations and how the focus of each organization changes diachronically. Besides its academic contribution, this study also demonstrates how, through the use of existing techniques with limited customization, digital technologies in the hands of the historian can augment and complement qualitative methods in bringing to light the themes and trends demonstrated in large bodies of historical documents.
Extension for Community Healthcare Outcomes (ECHO) Telementoring in the Military: Where We Are Now, Opportunities and Challenges
Authors: Katzman Joanna , Tomedi Laura , Swift Robin , Castillo Erick , Morrow Connie , Lutz Laurie , Galloway Kevin T , McCoy-Stafford Kimberly , Klein Zachary , Turner Greg , Beckman Darrick J , Terrell Jennifer , Forde Shannon , Martin Chamron , Morgan Sharon
Published: February 2021

Introduction

In collaboration with the ECHO (Extension for Community Healthcare Outcomes) Institute since 2012, the Army, Navy, and Air Force have developed medical teleECHO programs to address various health and safety issues affecting military personnel. This article describes and compares the current state of military teleECHOs as well as the growth and change over time.

Materials and Methods

This study evaluated continuing education units (CEUs) offered, average session attendance, and number of spoke sites for current military teleECHO programs across the service branches.

Results

Between 2012 and 2019, the military teleECHO initiative grew from one program to seven different teleECHO programs, covering topics from pain to diabetes to amputee care. Military ECHOs now provide training to 10 countries and 27 states in the United States. Between October 2018 and September 2019, the military ECHO programs provided a total of 51,769 continuing medical education (CME) hours to a total of 3,575 attendees from 223 spoke sites.

Conclusions

The military has successfully used the ECHO model to improve the health and safety of active-duty military, retirees, and dependents.
Application of counter-selectable marker PIGA in engineering designer deletion cell lines and characterization of CRISPR deletion efficiency
Authors: Li Donghui , Sun Xiaoji , Yu Fangzhou , Perle Mary Ann , Araten David , Boeke Jef D
Published: February 2021

The CRISPR/Cas9 system is a technology for genome engineering, which has been applied to indel mutations in genes as well as targeted gene deletion and replacement. Here, we describe paired gRNA deletions along the PIGA locus on the human X chromosome ranging from 17 kb to 2 Mb. We found no compelling linear correlation between deletion size and the deletion efficiency, and there is no substantial impact of topologically associating domains on deletion frequency. Using this precise deletion technique, we have engineered a series of designer deletion cell lines, including one with deletions of two X-chromosomal counterselectable (negative selection) markers, PIGA and HPRT1, and additional cell lines bearing each individual deletion. PIGA encodes a component of the glycosylphosphatidylinositol (GPI) anchor biosynthetic apparatus. The PIGA gene counterselectable marker has unique features, including existing single cell level assays for both function and loss of function of PIGA and the existence of a potent counterselectable agent, proaerolysin, which we use routinely for selection against cells expressing PIGA. These designer cell lines may serve as a general platform with multiple selection markers and may be particularly useful for large scale genome engineering projects such as Genome Project-Write (GP-write).
The Complement C4 Genetic Diversity in First Episode Psychosis of the OPTiMiSE Cohort
Authors: Mariaselvam Christina M , Wu Ching-Lien , Boukouaci Wahid , Richard Jean-Romain , Barau Caroline , Le Corvoisier Philippe ,   OPTiMiSE Study Group, Dazzan Paola , Egerton Alice , Pollak Thomas A , McGuire Philip , Rujescu Dan , Jamain Stéphane , Leboyer Marion , Tamouza Ryad
Published: February 2021

Recent findings implicate the complement C4 gene in gray matter loss in schizophrenia. In a large cohort of patients with first-episode psychosis (FEP), we aimed to (1) characterize the frequency of C4 gene copy number variations (CNVs) and HERV-K Ins/Del events as compared to that in healthy controls (HCs) and (2) evaluate whether C4 gene structural variants influence baseline clinical symptoms and treatment response to amisulpride. A total of 271 FEP subjects and 221 HCs were genotyped for C4 CNV and HERV-Ins/Del (C4A and C4B isoforms; C4-HERV structural forms [C4AL, C4AS, C4BL, C4BS] variations using droplet digital PCR. Overall, the gene frequencies of both C4 isoforms and C4-HERV structural forms did not significantly differ between groups. At the genotype level, we found that the C4 AL-AL-BL-BL genotype (AL-BL haplotype) was significantly more frequent in FEP as compared to HC. Apart from a marginal observation concerning the C4 AL-AL-BL-BL genotype (AL-BL haplotype), possibly reflecting a relationship with schizophrenia, we did not find any correlation between C4 genetic and clinical characteristics or treatment response in FEP.
Control and consent in the connected age: the work of contractors on transnational online education platforms
Authors: Lin Le
Published: February 2021

Drawing on ABCKID, one of the world’s largest online education platforms, and its six competitors, this paper rethinks control and consent of work in the platform economy. Falling into a new category of home-based virtual platforms, ABCKID has mobilized a group of American contractors (e.g. stay-at-home moms) who were previously marginalized in the US labor market. Using interviews, surveys and online data, I found that most ABCKID contractors show high levels of job satisfaction due to their relative gains. Furthermore, although ABCKID imposes strict and direct control over contractors’ work content and schedules, it opens new room for contractors to adapt to control. Contractors’ adaptive practices have also made the platform’s efforts to organize control as games less effective. I argue that consent of work on these platforms is not only a product of relative gains, but also a result of interactions between contractors’ adaptive practices and platforms’ direct controls.
Effects of feeding corn distillers dried grains with solubles diets without or with supplemental enzymes on growth performance of pigs: a meta-analysis
Authors: Jang Jae-Cheol , Zeng Zhikai , Urriola Pedro E , Shurson Gerald C
Published: February 2021

A meta-analysis was conducted to determine the effects of the dietary energy system (net energy or metabolizable energy), oil content of corn distillers dried grains with solubles (cDDGS), diet inclusion levels, and pig age on growth performance of pigs fed cDDGS-based diets. Mean differences of average daily gain (ADG), average daily feed intake (ADFI), and gain:feed (G:F) were calculated and expressed as a percentage change relative to feeding corn–soybean meal (SBM)- and cDDGS-based diets to nursery [body weight (BW) < 25 kg] and growing-finishing (BW > 25 kg) pigs, and to compare the effects of supplementing various types of exogenous enzymes without or with phytase on growth performance. A total of 27 studies with 106 growth performance observations were included in the cDDGS dataset, and 34 studies with 84 observations for enzyme responses in cDDGS diets were used in the enzyme dataset. Approximately, 64.7% of the observations showed no change, and 26.7% of observations showed a reduction in ADG, ADFI, and G:F when feeding cDDGS-based diets to the nursery and growing-finishing pigs compared with feeding corn–SBM-based diets. Furthermore, feeding cDDGS diets resulted in decreased (P < 0.01) mean difference of ADG (–4.27%) and G:F (–1.99%) for nursery pigs, and decreased (P < 0.01) mean difference of ADG (–1.68%) and G:F (–1.06%) for growing–finishing pigs. Every percentage unit increase in the inclusion level of cDDGS in growing–finishing pig diet was associated with a decrease (P < 0.01) in ADG (–0.10%) and ADFI (–0.09%). Feeding high oil (≥10% ether extract) cDDGS-based diets to pigs resulted in a 2.96% reduction in ADFI whereas feeding reduced-oil (<10% ether extract) cDDGS-based diets reduced G:F by 1.56% compared with pigs fed corn–SBM-based diets. Supplementation of exogenous enzymes improved (P < 0.05) the mean difference of ADG and G:F by 1.94% and 2.65%, respectively, in corn–SBM-based diets, and by 2.67% and 1.87%, respectively, in cDDGS diets. Supplementation of exogenous protease, enzyme cocktail, or xylanase improved (P < 0.05) ADG by 7.29%, 2.64%, and 2.48% in pigs fed corn–SBM-based diets, respectively. There were no differences between the dietary addition of single enzymes and enzyme combinations for any growth performance parameters in corn–SBM- or cDDGS-based diets. In conclusion, feeding cDDGS-based diets slightly reduces the growth performance of nursery and growing–finishing pigs, but supplementation of xylanase or enzyme cocktail can improve G:F of pigs fed cDDGS-based diets.
SubclonalCHD1deletion is more frequent in African American prostate cancers and associated with rapid disease progression and limited levels of homologous recombination deficiency
Authors: Diossy Miklos , Tisza Viktoria , Li Hua , Zhou Jia , Sztupinszki Zsofia , Young Denise , Nousome Darryl , Kuo Claire , Jiang Jiji , Chen Yongmei , Ebner Reinhard , Sesterhenn Isabell A. , Moncur Joel T. , Chesnut Gregory T. , Petrovics Gyorgy , Klus Gregory T. , Valcz Gabor , Nuzzo Pier Vitale , Ribli Dezso , Schina Aimilia , Börcsök Judit , Prosz Aurel , Krzystanek Marcin , Ried Thomas , Szuts David , Kaochar Salma , Pathania Shailja , D’Andrea Alan D. , Csabai Istvan , Srivastava Shiv , Freedman Matthew L , Dobi Albert , Spisak Sandor , Szallasi Zoltan
Published: February 2021

Chromodomain helicase DNA-binding protein 1 (CHD1) is frequently deleted in a subset of prostate cancers. We show here that subclonal deletion ofCHD1is nearly three times as frequent in prostate tumors of African American men than in men of European ancestry and it associates with rapid disease progression. We further show thatCHD1deletion is associated with only one type of the homologous recombination deficiency associated mutational signatures in prostate cancer. In prostate cancer cell line modelsCHD1deletion did not induce HRD as detected by RAD51 foci formation assay, which was consistent with the moderate increase of olaparib sensitivity.CHD1deficient prostate cancer cells, however, still showed markedly increased sensitivity to talazoparib, which could be effective for the treatment ofCHD1deficient tumors in the context of hormone therapy resistant prostate cancer.
Attentional Modulations of Alpha Power Are Sensitive to the Task-relevance of Auditory Spatial Information
Authors: Klatt Laura-Isabelle , Getzmann Stephan , Schneider Daniel
Published: February 2021

The topographical distribution of oscillatory power in the alpha band is known to vary depending on the current focus of spatial attention. Here, we investigated to what extend univariate and multivariate measures of post-stimulus alpha power are sensitive to the required spatial specificity of a task. To this end, we varied the perceptual load and the spatial demand in an auditory search paradigm. A centrally presented sound at the beginning of each trial indicated the to-be-localized target sound. This spatially unspecific pre-cue was followed by a sound array, containing either two (low perceptual load) or four (high perceptual load) simultaneously presented lateralized sound stimuli. In separate task blocks, participants were instructed either to report whether the target was located on the left or the right side of the sound array (low spatial demand) or to indicate the exact target location (high spatial demand). Univariate alpha lateralization magnitude was neither affected by perceptual load nor by spatial demand. However, an analysis of onset latencies revealed that alpha lateralization emerged earlier in low (vs. high) perceptual load trials as well as in low (vs. high) spatial demand trials. Finally, we trained a classifier to decode the specific target location based on the multivariate alpha power scalp topography. A comparison of decoding accuracy in the low and high spatial demand conditions suggests that the amount of spatial information present in the scalp distribution of alpha-band power increases as the task demands a higher degree of spatial specificity. Altogether, the results offer new insights into how the dynamic adaption of alpha-band oscillations in response to changing task demands is associated with post-stimulus attentional processing.
Rapid processing and quantitative evaluation of multicontrast EPImix scans for adaptive multimodal imaging
Authors: Váša František , Hobday Harriet , Stanyard Ryan A. , Daws Richard E. , Giampietro Vincent , O’Daly Owen , Lythgoe David J. , Seidlitz Jakob , Skare Stefan , Williams Steven C. R. , Marquand Andre F. , Leech Robert , Cole James H.
Published: February 2021

Current neuroimaging acquisition and processing approaches tend to be optimised for quality rather than speed. However, rapid acquisition and processing of neuroimaging data can lead to novel neuroimaging paradigms, such as adaptive acquisition, where rapidly processed data is used to inform subsequent image acquisition steps. Here we first evaluate the impact of several processing steps on the processing time and quality of registration of manually labelled T1-weighted MRI scans. Subsequently, we apply the selected rapid processing pipeline both to rapidly acquired multicontrast EPImix scans of 95 participants (which include T1-FLAIR, T2, T2*, T2-FLAIR, DWI & ADC contrasts, acquired in ∼1 minute), as well as to slower, more standard single-contrast T1-weighted scans of a subset of 66 participants. We quantify the correspondence between EPImix and single-contrast T1-weighted scans, using correlations between voxels and regions of interest across participants, measures of within- and between-participant identifiability as well as regional structural covariance networks. Furthermore, we explore the use of EPImix for the rapid construction of morphometric similarity networks. Finally, we quantify the reliability of EPImix-derived data using test-retest scans of 10 participants. Our results demonstrate that quantitative information can be derived from a neuroimaging scan acquired and processed within minutes, which could further be used to implement adaptive multimodal imaging and tailor neuroimaging examinations to individual patients.

Abstract Figure

Graphical abstract.
Creation of a single cell RNA seq meta-atlas to define human liver immune homeostasis
Authors: Rocque Brittany , Barbetta Arianna , Singh Pranay , Goldbeck Cameron , Helou Doumet Georges , Loh Yong-Hwee Eddie , Ung Nolan , Lee Jerry , Akbari Omid , Emamaullee Juliet
Published: February 2021

The liver is unique in both its ability to maintain immune homeostasis and in its potential for immune tolerance following solid organ transplantation. Single-cell RNA sequencing (scRNA seq) is a powerful approach to generate highly dimensional transcriptome data to understand cellular phenotypes. However, when scRNA data is produced by different groups, with different data models, different standards, and samples processed in different ways, it can be challenging to draw meaningful conclusions from the aggregated data. The goal of this study was to establish a method to combine ‘human liver’ scRNA seq datasets by 1) characterizing the heterogeneity between studies and 2) using the meta-atlas to define the dominant phenotypes across immune cell subpopulations in healthy human liver. Publicly available scRNA seq data generated from liver samples obtained from a combined total of 17 patients and ∼32,000 cells were analyzed. Liver-specific immune cells (CD45+) were extracted from each dataset, and immune cell subpopulations (myeloid cells, NK and T cells, plasma cells, and B cells) were examined using dimensionality reduction (UMAP), differential gene expression, and ingenuity pathway analysis. All datasets co-clustered, but cell proportions differed between studies. Gene expression correlation demonstrated similarity across all studies, and canonical pathways that differed between datasets were related to cell stress and oxidative phosphorylation rather than immune-related function. Next, a meta-atlas was generated via data integration and compared against PBMC data to define gene signatures for each hepatic immune subpopulation. This analysis defined key features of hepatic immune homeostasis, with decreased expression across immunologic pathways and enhancement of pathways involved with cell death. This method for meta-analysis of scRNA seq data provides a novel approach to broadly define the features of human liver immune homeostasis. Specific pathways and cellular phenotypes described in this human liver immune meta-atlas provide a critical reference point for further study of immune mediated disease processes within the liver.
Tree phylogenetic diversity supports nature’s contributions to people, but is at risk from human population growth
Authors: Davies T. Jonathan , Maurin Olivier , Yessoufou Kowiyou , Daru Barnabas H. , Bezeng Bezeng S. , Schaefer Hanno , Thuiller Wilfried , van der Bank Michelle
Published: February 2021

There is growing evidence for a link between biodiversity and ecosystem function, and for a correlation between human population and the species diversity of plants and animals in a region. Here, we suggest these relationships might not be independent. Using a comprehensive phylogeny of southern African trees and structural equation modelling, we show that human population density correlates with tree phylogenetic diversity and show that this relationship is stronger than the correlation with species richness alone. Further, we demonstrate that areas high in phylogenetic diversity support a greater diversity of ecosystem goods and services, indicating that the evolutionary processes responsible for generating variation among living organisms are also key to the provisioning of nature’s contributions to people. Our results raise the intriguing possibility that the history of human settlement in southern Africa may have been shaped, in part, by the evolutionary history of its tree flora. However, the correlation between human population and tree diversity generates a conflict between people and nature. Our study suggests that future human population growth may threaten the contributions to people provided by intact and phylogenetically diverse ecosystems.
Genomic evidence that governmentally producedCannabis sativapoorly represents genetic variation available in state markets
Authors: Vergara Daniela , Huscher Ezra L. , Keepers Kyle G. , Pisupati Rahul , Schwabe Anna L. , McGlaughlin Mitchell E. , Kane Nolan C.
Published: February 2021

The National Institute on Drug Abuse (NIDA) is the sole producer ofCannabisfor research purposes in the United States, including medical investigation. Previous research established that cannabinoid profiles in the NIDA varieties lacked diversity and potency relative to theCannabisproduced commercially. Additionally, microsatellite marker analyses have established that the NIDA varieties are genetically divergent form varieties produced in the private legal market. Here, we analyzed the genome of multipleCannabisvarieties from diverse lineages including two produced by NIDA, and we provide further support that NIDA’s varieties differ from widely available medical, recreational, or industrialCannabis. Furthermore, our results suggest that NIDA’s varieties lack diversity in the single copy portion of the genome, the maternally inherited genomes, the cannabinoid genes, and in the repetitive content of the genome. Therefore, results based on NIDA’s varieties are not generalizable regarding the effects ofCannabisafter consumption. For medical research to be relevant, material that is more widely used would have to be studied. Clearly, having research to date dominated by a single, non-representative source ofCannabishas hindered scientific investigation.
MEMS enabled miniaturized light-sheet microscopy with all optical control
Authors: Bakas Spyridon , Uttamchandani Deepak , Toshiyoshi Hiroshi , Bauer Ralf
Published: February 2021

We have designed and implemented a compact, cost-efficient miniaturised light-sheet microscopy system based on optical Microelectromechanical Systems (MEMS) scanners and tunable lenses. The system occupies a footprint of 20 × 28 × 13 cm3and combines off-the-shelf optics and optomechanics with 3D-printed structural and optical elements, and an economically costed objective lens, excitation laser and camera. All-optical volume scanning enables imaging of 340 × 190 × 60 µm3volumes with 0.25 vps and minimum lateral and axial resolution of 0.9 µm and 2.95 µm respectively. An open-top geometry allows imaging of samples on flat bottomed holders, allowing integration with microfluidic devices, multi-well plates and slide mounted samples, with applications envisaged in biomedical research and pre-clinical settings.
A computational approach to identify possible symbiotic mechanisms betweenKlebsiellaand the Mediterranean fly (Ceratitis capitata)
Authors: Franco L. Augusto , Pariente César Alberto Bravo
Published: February 2021

Nowadays, scientists develop multiple methods to control pests, like chemical control as the insecticides and biological control as the Sterile Insect Technique (SIT) to release infertile males produced by irradiation. This technique is complemented with research in the medfly’s(Ceratitis capitata)microbiota, this approach is based on the identification of molecular mechanisms from threeKlebsiellastrains using the reconstruction of metabolic pathways technique. We focus on the reconstruction of metabolic pathways involved in nitrogen metabolization because the bacteria are in charge of metabolizing the nitrogen compounds and make available for the medfly. We propose a pipeline to process the genome sequences the bacteria, reconstruct metabolic pathways and identify possible symbiont molecular mechanisms. The result of processing the biological data were ten pathways, six pathways produce L-Glutamate as final product, three pathways with ammonia product and one pathway was discarded because it was an internal pathway and don’t generate a metabolic product. Those pathways corresponding to L-Glutamate and ammonia metabolic products are part of nitrogen metabolism onKlebsiella, which shows that this metabolic process is one of the molecular mechanisms involved in symbiosis process betweenKlebsiellaand the medfly. Finally, by the results of the sequences analysis, in the medfly’s metamorphose the L-Glutamate are used in the synthesis of new proteins and the production of energy. The final consideration suggest that the pipeline propose can be used as first step to identify molecular mechanisms that can improve the production of industrial the medfly.
Structural and thermodynamic analyses of human TMED1 (p24γ1) Golgi dynamics
Authors: Mota Danielly C. A. M. , Mori Renan M. , Batista Mariana R. B. , Basso Luis G. M. , Cardoso Iara A. , Nonato M. Cristina , Costa-Filho Antonio J. , Mendes Luis F. S.
Published: February 2021

The transmembrane emp24 domain-containing proteins (TMED), also called p24 proteins, are members of a family of sorting receptors present in all representatives of the domain Eukarya and abundantly present in all subcompartments of the early secretory pathway, namely the endoplasmic reticulum (ER), the Golgi, and the intermediate compartment. Although essential during the bidirectional transport between the ER and the Golgi, there is still a lack of information regarding the TMEDs structure, oligomerization propensity, and biophysics of their interactions with the transport cargo. Here, we describe the first high-resolution structure of the Golgi dynamics (GOLD) domain of a TMED1 representative and its biophysical characterization in solution. The crystal structure showed a dimer formation that is also present in solution in a salt-dependent manner, suggesting that the GOLD domain can form homodimers even in the absence of the TMED1 coiled-coil region. A molecular dynamics description of the dimer stabilization, with a phylogenetic analysis of the residues important for the oligomerization and a model for the orientation towards the lipid membrane are also presented.
Thiophosphopeptides Instantly Targeting Golgi Apparatus and Selectively Killing Cancer Cells
Authors: Tan Weiyi , Zhang Qiuxin , Wang Jiaqing , Yi Meihui , He Hongjian , Xu Bing
Published: February 2021

Golgi apparatus is emerging as a key signaling hub of cells, but there are few approaches for targeting Golgi and selectively killing cancer cells. Here we show an unexpected result that changing an oxygen atom of the phosphoester bond in phospho-peptides by a sulfur atom enables instantly targeting Golgi apparatus (GA) and selectively killing cancer cells by enzymatic self-assembly. Specifically, conjugating cysteamine S-phosphate to the C-terminal of a self-assembling peptide generates a thiophospho-peptide. Being a substrate of alkaline phosphatase (ALP), the thiophosphopeptide undergoes rapid ALP-catalyzed dephosphorylation to form a thiopeptide that self-assembles. The thiophosphopeptide enters cells via caveolin-mediated endocytosis and macropinocytosis and instantly accumulates in GA because of dephosphorylation and formation of disulfide bonds in Golgi. Moreover, the thiophosphopeptide, targeting Golgi, potently and selectively inhibits cancer cells (e.g., HeLa) with the IC50 (about 3 μM), which is an order of magnitude more potent than that of the parent phosphopeptide. This work, as the first report of thiophospho-peptide for targeting Golgi, illustrates a new molecular platform for designing enzyme responsive molecules that target subcellular compartment for functions.
Stomach serosal arteries distinguish gastric regions of the rat
Authors: Jaffey Deborah M , Chesney Logan , Powley Terry L.
Published: February 2021

Because the stomachin situhas few distinctive surface features and changes shape dramatically with food intake, we have used microCT imaging to (1) characterize the pattern of arteries, potential landmarks, on the stomach wall and (2) evaluate how meal-related shape changes affect the size of the different regions. The stomach receives its blood supply primarily from two pairs of vessels, the gastric and gastroepiploic arteries. Each of the three regions of the stomach is delineated by a distinctive combination of arterial fields: Thecorpus, consistent with its dynamic secretory activity and extensive mucosa, is supplied by extensive arterial trees formed by the left and right gastric arteries. These major arteries course circularly from the lesser towards the greater curvature, distally along both left and right walls of the corpus, and branch rostrally to supply the region. The muscularantrumis characterized by smaller arterial branches arising primarily from the right gastroepiploic artery that follows the distal greater curvature and secondarily from small, distally directed arteries supplied by the large vessels of the left and right gastric arteries. Theforestomach, essentially devoid of mucosal tissue and separated from the corpus by the limiting ridge, is vascularized predominantly by a network of small arteries issued from the left gastroepiploic artery coursing around the proximal greater curvature, as well as from higher order and smaller branches issued by the gastric and celiac arteries. The regions of the stomach empty at different rates, thus changing the dimensions of the organ regions non-linearly.