bluuebunny/crossref_metadata_2025_split huggingface dataset:
SCCNV: a software tool for identifying copy number variation from single-cell whole-genome sequencing
Authors: Dong Xiao , Zhang Lei , Hao Xiaoxiao , Wang Tao , Vijg Jan 
Published: January 2019

AbstractBackgroundIdentification of de novo mutations from cell populations requires single-cell whole-genome sequencing (SCWGS). Although many experimental protocols of SCWGS have been developed, few computational tools are available for downstream analysis of different types of somatic mutations, including copy number variation (CNV).ResultsWe developed SCCNV, a software tool for detecting CNVs from whole genome-amplified single cells. SCCNV is a read-depth based approach with adjustment for the whole-genome amplification bias.ConclusionsWe demonstrate its performance by analyzing data collected from most of the single-cell amplification methods, including DOP-PCR, MDA, MALBAC and LIANTI. SCCNV is freely available at https://github.com/biosinodx/SCCNV.
Extrachromosomal circular DNA, microDNA, without canonical promoters produce short regulatory RNAs that suppress gene expression
Authors: Paulsen Teressa , Shibata Yoshiyuki , Kumar Pankaj , Dillon Laura , Dutta Anindya 
Published: January 2019

ABSTRACTInterest in extrachromosomal circular DNA (eccDNA) molecules has increased recently because of their widespread presence in normal cells across every species ranging from yeast to humans, their increased levels in cancer cells, and their overlap with oncogenic and drug-resistant genes. However, the majority of eccDNA (microDNA) are too small to carry protein coding genes. We have tested functional capabilities of microDNA, by creating artificial microDNA molecules mimicking known microDNA sequences and have discovered that they express functional small regulatory RNA including microRNA and novel si-like RNA. MicroDNA is transcribedin vitroandin vivoindependent of a canonical promoter sequence. MicroDNA which carry miRNA genes form transcripts which are processed into mature miRNA molecules, through the endogenous RNA-interference pathway, which repress a luciferase reporter gene as well as endogenous mRNA targets of the miRNA. Further, microDNA containing sequences of exons repress the endogenous gene from which the microDNA was derived through the formation of novel si-like RNA. We also show that endogenous microDNA associate with RNA polymerases subunits POLR2H and POLR3F. Together, these results suggest that microDNA may modulate gene expression through the production of both known and novel regulatory small RNA.
Visual interference can help and hinder memory: Capturing representational detail using the Validated Circular Shape Space
Authors: Li Aedan Y. , Fukuda Keisuke , Lee Andy C. H. , Barense Morgan D. 
Published: January 2019

AbstractAlthough we can all agree that interference induces forgetting, there is surprisingly little consensus regarding what type of interference most likely disrupts memory. We previously proposed that the similarity of interference differentially impacts the representational detail of color memory. Here, we extend this work by applying the Validated Circular Shape Space (Li et al., 2020) for the first time to a continuous retrieval task, in which we quantified both the visual similarity of distracting information as well as the representational detail of shape memory. We found that the representational detail of memory was systematically and differentially altered by the similarity of distracting information. Dissimilar distractors disrupted both fine- and coarse-grained information about the target, akin to memory erasure. In contrast, similar distractors disrupted fine-grained target information but increased reliance on coarse-grained information about the target, akin to memory blurring. Notably, these effects were consistent across two mixture models that each implemented a different scaling metric (either angular distance or perceived target similarity), as well as a parameter-free analysis that did not fit the mixture model. These findings suggest that similar distractors will help memory in cases where coarse-grained information is sufficient to identify the target. In other cases where precise fine-grained information is needed to identify the target, similar distractors will impair memory. As these effects have now been observed across both stimulus domains of shape and color, and were robust across multiple scaling metrics and methods of analyses, we suggest that these results provide a general set of principles governing how the nature of interference impacts forgetting.
Whole genome sequencing and comparative genomic analysis reveal novel allelic variations unique to a purple colored rice landrace (Oryza sativa ssp. indica cv. Purpleputtu)
Authors: Lachagari V. B. Reddy , Gupta Ravi , Lekkala Sivarama Prasad , Mahadevan Lakshmi , Kuriakose Boney , Chakravartty Navajeet , Katta A. V. S. Krishna Mohan , Santhosh Sam , Reddy Arjula R. , Thomas George 
Published: January 2019

AbstractPurpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait and associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with purple, red coloration of grain and other plant parts. Comparative genomic analysis of the whole genome sequence of Purpleputtu (PP) revels total of 3,200,951 variants including 67,774 unique variations were observed in PP when compared with 108 rice genomes. Multiple sequence alignment uncovered a 14bp deletion in Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species rufipogon and nivara. In addition, PP genome exhibits a well conserved a 4.5Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique SNPs compared to 3,024 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance and protection from harmful UV-B rays.
Acute ethanol intoxication induces preferred loss of presynaptic boutons devoid of mitochondria in vivo
Authors: Protzmann Jil , Jaiswal Astha , Rohr Karl , Kuner Thomas , Cambridge Sidney , Knabbe Johannes 
Published: January 2019

AbstractAcute alcohol intoxication is frequently observed in modern societies and carries a vast burden, ranging from traffic accidents to transient memory loss. Despite years of intense research, the effects of acute ethanol intoxication on brain function remain incompletely understood. Here, we studied the effect of acute ethanol intoxication on axonal organelle trafficking and presynaptic structure using in vivo two photon microscopy in anesthetized mice. After a single intraperitoneal injection of ethanol, inducing a blood alcohol concentration of roughly 250 mg/dl, the axonal mitochondrial mobility was doubled while dense core vesicle mobility remained unaffected. Simultaneously imaging mitochondria and presynaptic boutons revealed that unoccupied presynaptic boutons perished more frequently after ethanol exposure, while boutons stably occupied with mitochondria mostly persisted. Our results define a novel mechanism of ethanol action and may explain difficulties in permanently storing new memories after episodes of intense ethanol consumption with a loss of synapses.
Male clients of male sex workers in West Africa: A neglected high risk population
Authors: Kounta Cheick Haïballa , Sagaon-Teyssier Luis , Coulaud Pierre-Julien , Mora Marion , Maradan Gwenaelle , Bourrelly Michel , keita Abdoul Aziz , Yoro Stéphane-Alain Babo , Anoma Camille , Coulibaly Christian , Dah Elias Ter Tiero , Agbomadji Selom , Mensah Ephrem , Bernier Adeline , Couderc Clotilde , Keita Bintou Dembélé , Laurent Christian , Spire Bruno ,   the CohMSM Study Group
Published: January 2019

AbstractResearch on male clients of male sex workers (MCMSW) has been neglected for a long time globally. We aimed to characterize MCMSW and to identify factors associated with their sexual practices using data from the prospective cohort study CohMSM conducted in Burkina Faso, Côte d’Ivoire, Mali and Togo. Our study focused on HIV-negative men who have sex with other men (MSM) recruited between 06/2015 and 01/2018 by a team of trained peer educators. Scheduled study visits at 6, 12 and 18 months included medical examinations, HIV screening, risk-reduction counselling and face-to-face interviews to collect information on their sociodemographic characteristics, sexual behaviours, and HIV risk-reduction strategies (HIV-RRS). Three stigmatization sub-scores were constructed (experienced, perceived and internalized). Mixed-effects logistic regression was used for data analysis. Of the 280 participants recruited at baseline, 238, 211 and 118, respectively, had a follow-up visit at 6, 12 and 18 months. Over a total of 847 visits, 47 transactional sex (TS) encounters were reported by 38 MCMSW (13.6%). Of the latter, only one participant reported systematic TS (2.6%), 18 (47.4 %) stopped reporting TS after baseline, and 6 (15.8%) reported TS after baseline. Thirteen participants (34.2 %) reported occasional TS. After adjusting for country of study and age, the following self-reported factors were associated with a greater likelihood of being MCMSW: protected anal sex, exclusively insertive anal sex with male sexual partners, avoidance of sex after consuming psychoactive products and experiencing stigmatization (all during the previous 6 months). The majority of MCMSW in this study employed HIV-RRS with male sexual partners, including engaging in protected anal sex, avoidance of sex when consuming psychoactive products, and practising exclusively insertive anal sex.
Mapping the lineage relationship between CXCR5+ and CXCR5- CD4+ T cells in HIV infected human lymph nodes
Authors: Del Alcazar Daniel , Wang Yifeng , He Chenfeng , Wendel Ben S. , Del Río-Estrada Perla M. , Lin Jerome , Ablanedo-Terrazas Yuria , Malone Michael J , Hernandez Stefany M. , Frank Ian , Naji Ali , Reyes-Terán Gustavo , Jiang Ning , Su Laura F. 
Published: January 2019

SummaryCXCR5 is a key surface marker expressed on follicular helper T (TFH) cells. We report here B cell help functionality in a population of CD4+ T cells isolated from primary human lymph nodes (LN) that lacked CXCR5 expression. This CXCR5- subset is distinguished from other CXCR5- CD4+ T cells by high PD-1 expression. Accumulation of CXCR5-PD-1+ T cells correlated with peripheral CD4+ T cell depletion and an increase in T-bet+ B cells in the LN, highlighting these atypical CD4+ T cells as a key component of lymphoid dysregulation during chronic HIV infection. By interrogating the phenotypic heterogeneity, functional capacity, TCR repertoire, transcriptional profile, and epigenetic state of CXCR5-PD-1+ T cells, we showed that CXCR5-PD-1+ T cells are related to CXCR5+PD-1+ T cells and provided evidence for the down regulation of CXCR5 following cell division as one mechanism for the absence of CXCR5 expression. Notably, CXCR5-PD-1+ T cells exhibited a migratory transcriptional program and contributed to circulating CXCR5-PD-1+ T cells with B cell help functionality in the peripheral blood. Thus, these data link LN pathology to circulating T cells and expand the current understanding on T cell diversity in the regulation of B cell responses during chronic inflammation.High dimensional profiling of activated CD4+ T cells in HIV infected lymph nodes revealed an accumulation of a CXCR5 negative subset.CXCR5-PD-1+CD4+ T cells exhibited TFH-like protein expression and function.CXCR5-PD-1+CD4+ T cells are related to TFH cells by clonal lineage and epigenetic similarity.CXCR5-PD-1+CD4+ T cells upregulate a migratory gene program and contribute to circulating T cells with B cell help functionality
The suboptimality of perceptual decision making with multiple alternatives
Authors: Yeon Jiwon , Rahnev Dobromir 
Published: January 2019

AbstractIt is becoming widely appreciated that human perceptual decision making is suboptimal but the nature and origins of this suboptimality remain poorly understood. Most past research has employed tasks with two stimulus categories, but such designs cannot fully capture the limitations inherent in naturalistic perceptual decisions where choices are rarely between only two alternatives. We conducted four experiments with tasks involving multiple alternatives and used computational modeling to determine the decision-level representation on which the perceptual decisions were based. The results from all four experiments pointed to the existence of robust suboptimality such that most of the information in the sensory representation was lost during the transformation to a decision-level representation. These results reveal severe limits in the quality of decision-level representations for multiple alternatives and have strong implications about perceptual decision making in naturalistic settings.
Constrained purchase decision-making process at the base of the pyramid
Authors: Choudhury Nanda , Mukherjee Srabanti , Datta Biplab 
Published: January 2019

Purpose
The purpose of this paper is to examine the factors affecting decision-making at the BoP and propose a framework of the consumer decision-making process at the base of the pyramid (BoP).

Design/methodology/approach
The qualitative research design was adopted to collect primary data. Data collected through the in-depth semi-structured interviews of the 48 BoP consumers in Kolkata and Kharagpur (India) were subjected to grounded theory analysis for theory development.

Findings
This study reveals that consumer vulnerability affects the decision-making process and the transaction cost at BoP level. It was observed that the consumers at the BoP make constrained choices due to their vulnerability and try to minimise transaction cost while selecting the retails. The constrained retail choice leads to a limited selection of products and brands.

Originality/value
This study, for the first time, has investigated the decision-making process for BoP consumers in detail. As a pioneering attempt, it sheds light on some new factors including consumer vulnerability and transaction cost that have an impact on the consumer decision-making process.
Knowledge management in franchising: a research agenda
Authors: Iddy Judith Jacob , Alon Ilan 
Published: January 2019

PurposeThis paper aims to offer a comprehensive systematic review of knowledge management (KM) in franchising literature over the past 29 years.Design/methodology/approachBy means of bibliometric citation analysis, ISI Web of Science (WoS) database is used to analyze articles from 1990-2018. A total of 169 articles by 369 authors across 40 countries published in 113 journals from 200 institutions were clustered and examined through HistCites and VOSviewer.FindingsThe exploration of KM in franchising is associated with 3 factors: governance structure; performance outcome; and franchise network growth. The findings also reveal that KM in franchising is still an emerging discipline encompassing conflicting results which offer potential for future research.Research limitations/implicationsIdentified research gaps and contradicting views in the literature offer opportunities for researchers to contribute to this research domain by empirically testing the role of absorptive capacity, replication vs adaptation strategies and new franchising formats, such as micro/social franchising.Originality/valueThis study is unique in its examination of KM in franchising. It also highlights the value of knowledge in franchise chain performance.
Yoghurt‐type beverage with partial substitution of milk by a chickpea extract: Effect on physicochemical and flow properties
Authors: Aguilar‐Raymundo Victoria Guadalupe , Vélez‐Ruiz Jorge Fernando 
Published: January 2019

The objective of this study was to determine the evolution of physicochemical and flow properties of a yoghurt‐type beverage partially replaced with a chickpea extract over a period of 22 days. From two chickpea extracts, Blanco Noroeste was selected for its higher protein content. Six yoghurt‐type formulations were prepared, stored at 4 °C and analysed on days 1, 8, 15 and 22. pH was 4.24–4.75, while brightness was 81.7–94.5. Flow properties of the yoghurt‐type exhibited a non‐Newtonian behaviour. From three formulations that underwent sensory evaluation, the 30:70 mix obtained the highest acceptation. This yoghurt‐type beverage exhibited characteristics similar to natural yoghurt.
Relapse patterns and predictors of IgG4‐related diseases involved with autoimmune pancreatitis: A single‐center retrospective study of 115 patients
Authors: Miki Masami , Fujimori Nao , Oono Takamasa , Kawabe Ken , Ohno Akihisa , Matsumoto Kazuhide , Teramatsu Katsuhito , Tachibana Yuichi , Ogawa Yoshihiro 
Published: January 2019

ObjectiveAutoimmune pancreatitis is an autoimmune disorder accompanied by clinicopathological manifestations that have been established as immunoglobulin (IgG)4‐related diseases (IgG4‐RD). Other IgG4‐RD are often involved with autoimmune pancreatitis. They sometimes relapse despite a favorable response to steroid therapy. This study aimed to clarify the patterns and risk factors for extrapancreatic relapse.MethodsWe reviewed the data of 115 patients diagnosed with definite autoimmune pancreatitis type 1 and followed up for > 1 year. We analyzed two items: the timing and pattern of extrapancreatic relapse, and risk factors for relapse with three common manifestations: IgG4‐related sclerosing cholangitis (SC), IgG4‐related dacryoadenitis and sialadenitis (DS), and IgG4‐related retroperitoneal fibrosis (RF).ResultsRemission was achieved in all patients, except one. The extrapancreatic relapse rates were 11.0%, 19.7%, and 40% within 3, 5, and 10 years, respectively. Of 26 patients with extrapancreatic relapse, nine (34.6%) relapsed with a new IgG4‐RD. Based on multivariate analysis, the interval between symptom onset and steroid initiation, and the presence of RF at onset were significant risk factors for relapse with SC and RF, respectively.ConclusionsOur results indicate that they may be various extrapancreatic relapse patterns especially in autoimmune pancreatitis with other organ involvement. Patients with a delayed initiation of steroids or RF at onset should be carefully followed up as high‐risk groups for SC and RF relapse.
Point‐Combination Transect (PCT): Incorporation of small underwater cameras to study fish communities
Authors: Widmer Lukas , Heule Elia , Colombo Marco , Rueegg Attila , Indermaur Adrian , Ronco Fabrizia , Salzburger Walter 
Published: January 2019

Abstract

Available underwater visual census (UVC) methods such as line transects or point count observations are widely used to obtain community data of underwater species assemblages, despite their known pit‐falls. As interest in the community structure of aquatic life is growing, there is need for more standardized and replicable methods for acquiring underwater census data.

Here, we propose a novel approach, Point‐Combination Transect (PCT), which makes use of automated image recording by small digital cameras to eliminate observer and identification biases associated with available UVC methods. We conducted a pilot study at Lake Tanganyika, demonstrating the applicability of PCT on a taxonomically and phenotypically highly diverse assemblage of fishes, the Tanganyikan cichlid species‐flock.

We conducted 17 PCTs consisting of five GoPro cameras each and identified 22,867 individual cichlids belonging to 61 species on the recorded images. These data were then used to evaluate our method and to compare it to traditional line transect studies conducted in close proximity to our study site at Lake Tanganyika.

We show that the analysis of the second hour of PCT image recordings (equivalent to 360 images per camera) leads to reliable estimates of the benthic cichlid community composition in Lake Tanganyika according to species accumulation curves, while minimizing the effect of disturbance of the fish through SCUBA divers. We further show that PCT is robust against observer biases and outperforms traditional line transect methods.
No increased pain among opioid‐dependent individuals treated with extended‐release naltrexone or buprenorphine‐naloxone: A 3‐month randomized study and 9‐month open‐treatment follow‐up study
Authors: Latif Zill‐e‐Huma , Solli Kristin K. , Opheim Arild , Kunoe Nikolaj , Benth Jūratė Š. , Krajci Peter , Sharma‐Haase Kamni , Tanum Lars 
Published: January 2019

Background and ObjectivesIt is presently unclear whether extended‐release naltrexone hydrochloride treatment induces pain or aggravates existing pain among individuals with opioid use disorders. We assessed changes in pain among individuals receiving treatment with either extended‐release naltrexone hydrochloride or buprenorphine‐naloxone hydrochloride.MethodsThis randomized prospective open‐label clinical study included 143 participants (aged 18–60 years) with opioid dependencies, recruited from outpatient addiction clinics at five urban hospitals in Norway. After in‐patient detoxification from opioids, patients were randomized to 12‐week treatment with either long‐acting naltrexone (380 mg intramuscularly injected every four weeks) or buprenorphine‐naloxone (flexible 4–16 mg sublingual doses daily). This phase was followed by a 9‐month open‐treatment study with the participant's choice of either naltrexone or buprenorphine‐naloxone. Changes in pain were assessed every 4 weeks using the Norwegian Short‐Form of McGill Pain Questionnaire.ResultsThroughout the study period, we found no increase in mean sensory pain, affective pain, or present pain intensity on the McGill Pain Questionnaire, in either treatment group, including the subgroups of participants with chronic pain. Participants who switched from buprenorphine‐naloxone to extended‐release naltrexone treatment after week 12 reported no increase in pain intensity during longer‐term treatment. Women experienced significantly more affective pain symptoms than men (p = .01).Discussion and ConclusionsAmong individuals with opioid use disorder, switching from daily opioid use to long‐acting naltrexone did not induce pain, or aggravate mild‐to‐moderate chronic pain.Scientific SignificanceIn opioid‐dependent individuals, mild‐to‐moderate chronic pain was not influenced by opioid agonist or antagonist treatment.Trial RegistrationClinicaltrials.gov #NCT01717963, first registered: Oct 28, 2012. Protocol version # 3C, June 12th 2012. (Am J Addict 2018;XX:1–9)