bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of farmers/livestock groups institutional characteristics in barru regency
Authors: Raisa D M , Sirajuddin S N , Abdullah A 
Published: June 2020

Abstract
This study aims to analyze the institutional characteristics of farmer/livestcok groups consists of group binding element aspects, and the groups function is in supporting institutional groups of farmers/livestock groups. The research type used is quantitative descriptive by survey approach with qualitative research data types that are quantified based on Likert measurement scale. This research was conducted in Barru Sub-District, Barru Regency, South Sulawesi. Population in this study is all beef cattle farmers who are member of farmer/livestock groups in their area with beginner group ability class, advanced, intermediate, main. The number of research samples is 91 people. Data analysis used is descriptive statistics. The results showed that the institution of farmer/livestock groups in Barru District, Barru Regency viewed from the aspect of group institutional characteristics had not been able to support groups success in achieve the common goal because there were still many groups with higher class status but the activities carried out according to the institutional function of farmer/livestock groups is unfulfilled.
Financial feasibility analysis of skipjack tuna (Katsuwonus pelamis) catching in Bone bay, South Sulawesi, Indonesia
Authors: Amiluddin  , Baso A , Najamuddin  , Hamzah  
Published: June 2020

Abstract
Skipjack tuna (Katsuwonus pelamis) which was a type of fish not only a household consumption commodity in Indonesia, but also a superior commodity as an export from the fisheries sector in Indonesia. This study aims to analyze the financial feasibility of the skipjack tuna catching use pole and line, and hand line fishing gear in Bone bay, conducted from January to December 2018 in Luwu Regency and Sinjai Regency. The method used in this study is the survey research method with cluster random sampling of skipjack tuna fishermen. The data analysis used financial feasibility analysis consists of profit analysis and investment analysis includes Net Present Value (NPV), Net Benefit-Cost Ratio (Net B/C), and Internal Rate of Return (IRR). The results show that, in one year of catching skipjack tuna in Bone bay waters, the highest profit was found in fishing businesses use pole and line fishing gear of IDR 2,720,662,561. For fishing use hand line gear get profit in one year of IDR 450,810,385. From the acquisition of each investment analysis used above shows an analysis of the investment criteria obtained NPV > 0, net B/C > 1 and IRR > the prevailing interest rate (12%), so it can be concluded that these two types of fishing gear are feasible to be developed.
Interaction of integrating land use systems on pig farming systems, West Papua-Indonesia; worth or worse?
Authors: Iyai D A , Ako A , Sirajuddin S N , Budiman  
Published: June 2020

Abstract
In the pattern of livestock keeping systems, livestock can have free access path to natural resources such as forests, scrubs, water, natural shading, wastes, and residues. How they use and do interact with land use systems particularly the pigs, become the focus of this assessment. the study areas will cover four districts, i.e. Warmare, Prafi, Masni and Sidey. The total areas of study therefore is 1,022.67 km2 (102,266.54 ha). Data collected from BPS board of Manokwari, Papua Barat. Data were analyzed using Statistical descriptive and shown in tables. Pictures were drawn using Arc GIS and Microsoft Visio. There are 11 types of land use systems which have roles in ecosystem and livestock-human interaction. Land use was dominated by tropical forest and followed by oil palm plantation, communal land, transmigrate areas and arable land. Beef cattle present dominantly the land use systems in agro-complex of Prafi, followed by pigs and goat. Further study is needed to prove the effect of interaction on sustainability indicators, i.e. society, economic and environment.
SATB2 in Neoplasms of Lung, Pancreatobiliary, and Gastrointestinal Origins
Authors: De Michele Simona , Remotti Helen E , Del Portillo Armando , Lagana Stephen M , Szabolcs Matthias , Saqi Anjali 
Published: June 2020

Abstract

Objectives
Special AT-rich binding protein 2 (SATB2) immunohistochemistry (IHC) has high sensitivity and specificity for colorectal adenocarcinoma (CRC), but data on its expression in specific subsets of pulmonary, gastric, small bowel, and pancreatobiliary adenocarcinomas (ADCAs) are relatively limited or discordant. We assessed SATB2 expression in a large cohort of ADCAs from these sites to determine its reliability in distinguishing CRC from them.

Methods
SATB2 IHC was performed on 335 neoplasms, including 40 lung ADCAs, 165 pancreatobiliary neoplasms (34 intraductal papillary mucinous neoplasms [IPMNs], 19 pancreatic ADCAs, 112 cholangiocarcinomas [CCs]), and 35 gastric, 13 small bowel, 36 ampullary (AMP), and 46 CRC ADCAs. The cases were evaluated for positivity (defined as ≥5% nuclear staining), and an H-score was calculated based on the percentage of SATB2+ cells and staining intensity. Analysis was performed to determine the optimal H-score threshold to separate CRC and non-CRC.

Results
SATB2 was positive in 3% of lung, 2% of CC, 17% of gastric, 38% of small bowel, and 6% of AMP ADCAs. All pancreatic ADCA/IPMNs were negative, and 87% CRCs were positive.

Conclusions
SATB2 is not entirely specific for colorectal origin and can be expressed in a subset of gastrointestinal ADCAs. It is most useful in the differential of CRC vs lung and pancreatobiliary ADCAs.
The Southern and Western Prehistory of “Liberty of Contract”: Revisiting the Path to Lochner in Light of the New History of American Capitalism
Authors: Clark Gabrielle E 
Published: June 2020

Abstract
This article examines the local legal histories of two “liberty of contract” constitutional disputes prior to Lochner in the South and West: Allgeyer v. Louisiana (1897) and Holden v. Hardy (1898). Drawing inspiration from the new history of American capitalism literature that has recently rethought the genesis of the modern American economy through a Southern and Western lens, this article argues that we have yet to fully grasp the relationship between uneven state development politics and economic rights jurisprudence under American constitutional law. In so doing, I build a new narrative that takes into account development politics, Louisiana lawyers with roots in the Confederacy, and Western Populist constitution-makers to rethink the origins and development of a doctrine that arguably continues to shape the modern world.
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data
Authors: Sturm Gregor , Szabo Tamas , Fotakis Georgios , Haider Marlene , Rieder Dietmar , Trajanoski Zlatko , Finotello Francesca 
Published: June 2020

Abstract

Summary
Advances in single-cell technologies have enabled the investigation of T-cell phenotypes and repertoires at unprecedented resolution and scale. Bioinformatic methods for the efficient analysis of these large-scale datasets are instrumental for advancing our understanding of adaptive immune responses. However, while well-established solutions are accessible for the processing of single-cell transcriptomes, no streamlined pipelines are available for the comprehensive characterization of T-cell receptors. Here, we propose single-cell immune repertoires in Python (Scirpy), a scalable Python toolkit that provides simplified access to the analysis and visualization of immune repertoires from single cells and seamless integration with transcriptomic data.

Availability and implementation
Scirpy source code and documentation are available at https://github.com/icbi-lab/scirpy.

Supplementary information
Supplementary data are available at Bioinformatics online.
Functional Connectivity within and beyond the Face Network Is Related to Reduced Discrimination of Degraded Faces in Young and Older Adults
Authors: Grady Cheryl L , Rieck Jenny R , Nichol Daniel , Garrett Douglas D 
Published: June 2020

Abstract
Degrading face stimuli reduces face discrimination in both young and older adults, but the brain correlates of this decline in performance are not fully understood. We used functional magnetic resonance imaging to examine the effects of degraded face stimuli on face and nonface brain networks and tested whether these changes would predict the linear declines seen in performance. We found decreased activity in the face network (FN) and a decrease in the similarity of functional connectivity (FC) in the FN across conditions as degradation increased but no effect of age. FC in whole-brain networks also changed with increasing degradation, including increasing FC between the visual network and cognitive control networks. Older adults showed reduced modulation of this whole-brain FC pattern. The strongest predictors of within-participant decline in accuracy were changes in whole-brain network FC and FC similarity of the FN. There was no influence of age on these brain-behavior relations. These results suggest that a systems-level approach beyond the FN is required to understand the brain correlates of performance decline when faces are obscured with noise. In addition, the association between brain and behavior changes was maintained into older age, despite the dampened FC response to face degradation seen in older adults.
Increased Protection of Earlier Use of Immunoprophylaxis in Preventing Perinatal Transmission of Hepatitis B Virus
Authors: Huang Hongyu , Xu Chenyu , Liu Lanhua , Chen Liping , Zhu Xiaoqin , Chen Jie , Feng Jing , Chen Tingmei , Xu Biao , Yang Jishi , Xu Biyun , Pan Mingjie , Dai Yimin , Hu Yali , Zhou Yi-Hua 
Published: June 2020

Abstract

Background
Passive-active immunoprophylaxis against mother-to-child transmission (MTCT) of hepatitis B virus (HBV) recommends administering hepatitis B immunoglobulin (HBIG) and birth-dose hepatitis B vaccine in infants within 12 or 24 hours after birth. With this protocol, MTCT of HBV still occurs in 5–10% infants of HBV-infected mothers with positive hepatitis B e antigen (HBeAg). The present study aimed to investigate whether earlier administration of HBIG and hepatitis B vaccine after birth can further increase protection efficacy.

Methods
We conducted a prospective, multi-center observational study in infants born to mothers with HBV infection, in whom neonatal HBIG and birth dose hepatitis B vaccine were administered within one hour after birth. The infants were followed up for HBV markers at 7–14 months of age.

Results
A total of 1140 pregnant women with HBV were enrolled, and 982 infants (9 twins) of 973 mothers were followed up at 9.6 ± 1.9 months of age. HBIG and birth-dose vaccine were administered in newborn infants within a median of 0.17 (0.02–1.0) hours after birth. The overall rate of MTCT was 0.9% (9/982), with none (0%) of the 607 infants of HBeAg-negative mothers and 9 (2.4%) of 375 infants of HBeAg-positive mothers acquiring HBV. All 9 HBV-infected infants were born to mothers with HBV DNA &gt;2.75 × 106 IU/mL. Maternal HBV DNA levels &gt;2 × 106 IU/mL were an independent risk factor (odds ratio, 10.627; 95% confidence interval, 2.135–∞) for immunoprophylaxis failure.

Conclusions
Earlier use (within 1 hour after birth) of HBIG and hepatitis B vaccine can provide better protection efficacy against MTCT of HBV.
Rusty Blackbirds select areas of greater habitat complexity during stopover
Authors: Wright James R , Powell Luke L , Matthews Stephen N , Tonra Christopher M 
Published: June 2020

AbstractThe Rusty Blackbird (Euphagus carolinus) is a widespread, uncommon migrant that has experienced heavy population declines over the last century. This species can spend over a quarter of their annual cycle on migration, so it is important to determine their habitat requirements during stopover events to inform effective conservation planning. We assessed their habitat selection at an important stopover site in northern Ohio during both fall and spring migration. Since stopover habitat selection is scale-dependent, we investigated both patch-scale (between patches) and fine-scale (within a patch) selection using radio telemetry to locate foraging and roosting flocks, and compared habitat variables between used and available points across the study site. At the patch scale, we found that birds preferred dogwood–willow swamp, low-lying forest patches, and areas of greater habitat complexity for foraging in both seasons. At the fine scale, spring migrants foraged closer to habitat edges than random, and preferred areas with more wet leaf litter and shallow water, and less grass cover. Fall migrants also preferred shallow water and leaf litter cover, and avoided areas with dense grass, forbs, and herbaceous shrub cover. By contrast, birds consistently roosted in dense stands of emergent Phragmites or Typha marsh, suggesting that the best stopover or staging sites are those with a matrix of different wetland habitats. Although the migratory range of Rusty Blackbirds is currently dominated by agricultural development, our results suggest that fragmented landscapes can still provide adequate habitat for migrants if the available land is managed for a variety of wet habitat types.
Whole Blood Profiling of T-cell-Derived microRNA Allows the Development of Prognostic models in Inflammatory Bowel Disease
Authors: Kalla R , Adams A T , Ventham N T , Kennedy N A , White R , Clarke C , Ivens A , Bergemalm D , Vatn S , Lopez-Jimena B ,   IBD Character Consortium, Ricanek P , Vatn M H , Söderholm Johan D , Gomollón F , Nowak J K , Jahnsen J , Halfvarson J , McTaggart S , Ho G T , Buck A , Satsangi J 
Published: June 2020

Abstract

Background
MicroRNAs [miRNAs] are cell-specific small non-coding RNAs that can regulate gene expression and have been implicated in inflammatory bowel disease [IBD] pathogenesis. Here we define the cell-specific miRNA profiles and investigate its biomarker potential in IBD.

Methods
In a two-stage prospective multi-centre case control study, next generation sequencing was performed on a discovery cohort of immunomagnetically separated leukocytes from 32 patients (nine Crohn’s disease [CD], 14 ulcerative colitis [UC], eight healthy controls) and differentially expressed signals were validated in whole blood in 294 patients [97 UC, 98 CD, 98 non-IBD, 1 IBDU] using quantitative PCR. Correlations were analysed with phenotype, including need for early treatment escalation as a marker of progressive disease using Cox proportional hazards.

Results
In stage 1, each leukocyte subset [CD4+ and CD8+ T-cells and CD14+ monocytes] was analysed in IBD and controls. Three specific miRNAs differentiated IBD from controls in CD4+ T-cells, including miR-1307-3p [p = 0.01], miR-3615 [p = 0.02] and miR-4792 [p = 0.01]. In the extension cohort, in stage 2, miR-1307-3p was able to predict disease progression in IBD (hazard ratio [HR] 1.98, interquartile range [IQR]: 1.20–3.27; logrank p = 1.80 × 10–3), in particular CD [HR 2.81; IQR: 1.11–3.53, p = 6.50 × 10–4]. Using blood-based multimarker miRNA models, the estimated chance of escalation in CD was 83% if two or more criteria were met and 90% for UC if three or more criteria are met.

Interpretation
We have identified and validated unique CD4+ T-cell miRNAs that are differentially regulated in IBD. These miRNAs may be able to predict treatment escalation and have the potential for clinical translation; further prospective evaluation is now indicated.
Metformin Use Is Associated with a Lower Risk of Inflammatory Bowel Disease in Patients with Type 2 Diabetes Mellitus
Authors: Tseng Chin-Hsiao 
Published: June 2020

Abstract

Aim
Our aim was to compare the risk of developing inflammatory bowel disease [IBD] between ever users and never users of metformin.

Methods
Patients with newly diagnosed type 2 diabetes mellitus from 1999 to 2005 were enrolled from Taiwan’s National Health Insurance. A total of 340 211 ever users and 24 478 never users who were free from IBD on January 1, 2006 were followed up until December 31, 2011. Hazard ratios were estimated by Cox regression incorporating the inverse probability of treatment weighting using a propensity score.

Results
New-onset IBD was diagnosed in 6466 ever users and 750 never users. The respective incidence rates were 412.0 and 741.3 per 100 000 person-years and the hazard ratio for ever vs never users was 0.55 [95% confidence interval: 0.51–0.60]. A dose–response pattern was observed while comparing the tertiles of cumulative duration of metformin therapy to never users. The respective hazard ratios for the first [&lt;26.0 months], second [26.0–58.3 months] and third [&gt;58.3 months] tertiles were 1.00 [0.93–1.09], 0.57 [0.52–0.62] and 0.24 [0.22–0.26]. While patients treated with oral antidiabetic drugs [OADs] without metformin were treated as a reference group, the hazard ratios for patients treated with OADs with metformin, with insulin without metformin [with/without other OADs] and with insulin and metformin [with/without other OADs] were 0.52 [0.42–0.66], 0.95 [0.76–1.20] and 0.50 [0.40–0.62], respectively.

Conclusion
A reduced risk of IBD is consistently observed in patients with type 2 diabetes mellitus who have been treated with metformin.
EMF awareness in the Japanese EFL/EMI context
Authors: Ishikawa Tomokazu 
Published: June 2020

AbstractThe notion of English as a multilingua franca (EMF) positions English within multilingualism, and EMF awareness prepares students to communicate effectively in this multilingual world of mobility. The present paper explores how, if ever, EMF-aware pedagogic intervention influences Japanese students’ perceptions of their communicative practices, particularly for English-major undergraduates in L1-shared classrooms. This intervention was made by providing opportunities for participants to engage in EMF and by examining their first-hand experiences and published EMF communication extracts in the classrooms. Empirical data from an open-ended questionnaire demonstrate that multilingual and transmodal accommodation was a way for them to notice and take advantage of global networks, develop capability and confidence in communication, and foster sensitivity to interactants’ backgrounds. The data also illustrate the invaluable role of individual multilingual experiences as classroom ‘materials’, and suggest that discussing these experiences potentially turns L1-shared classrooms into EMF scenarios through foregrounding students’ multilingual repertoires.
Extracellular and intracellular DNA for bacterial profiling of long-ripened cheeses
Authors: Bardelli Tommaso , Rossetti Lia , Zago Miriam , Carminati Domenico , Giraffa Giorgio , Tidona Flavio 
Published: June 2020

ABSTRACT
A novel approach was developed to extract the extracellular DNA (eDNA), i.e. the free DNA outside the microbial cell, compared to the intracellular DNA (iDNA). The two DNA fractions were investigated in seven long-ripened cheeses. Among different buffer solutions tested, EDTA 0.5 M at pH 8 enabled a mild homogenization of cheese samples and the highest eDNA recovery. The extraction protocol was tested on single strains of lactic acid bacteria characterizing many Italian long-ripened cheeses, such as Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus rhamnosus. The method resulted suitable for eDNA extraction because it minimized cell-lysis, avoiding the leakage of iDNA from the cells. The yields of eDNA, ranging from 0.01 to 0.36 µg g−1 cheese, were generally higher than the iDNA, indicating that autolytic phenomena prevailed over intact cells after 8–12 months of ripening. In four of the seven cheeses, the same LAB species were detected in the eDNA and iDNA fractions by length-heterogeneity PCR, while in the remaining three samples, a higher number of species was highlighted in the eDNA compared to the corresponding iDNA. The sequential extraction of eDNA and iDNA can be applied to obtain additional information on the composition of the bacterial community in long-aged cheeses.
Candida albicans Mrv8, is involved in epithelial damage and biofilm formation
Authors: Costa Anna Carolina Borges Pereira , Back-Brito Graziella Nuernberg , Mayer François L , Hube Bernhard , Wilson Duncan 
Published: June 2020

ABSTRACT
Candida albicans is the most common human fungal pathogen that can cause superficial and deep-seated infections in susceptible individuals. Despite its medical importance, the vast majority of C. albicans genes remain of unknown function. Here, we report a role for the lineage-specific gene, MRV8, in host pathogen interactions, mycelial microcolony maturation and biofilm formation. In silico analysis indicated that MRV8 encodes a four-pass transmembrane protein unique to the closely related pathogens C. albicans and Candida dubliniensis. Deletion of MRV8 did not affect C. albicans adherence to, or initial invasion into human oral epithelia, but inhibited mycelial development and strongly reduced epithelial damage. mrv8Δ/Δ cells exhibited a media-dependent defect in biofilm formation and mutant biofilm metabolic activity was enhanced by cyclosporin A. mrv8Δ/Δ biofilms were more tolerant to treatment with caspofungin, but not to fluconazole or amphotericin B. Co-stimulation with calcium chloride and calcofluor white rescued biofilm growth in the presence of caspofungin, and this rescue-effect was Mrv8-dependent. Together, our data demonstrate an important role for a lineage-specific gene (MRV8) in C. albicans biofilm formation, drug tolerance and host–pathogen interactions.
Development of a Novel Mind–Body Activity and Pain Management Program for Older Adults With Cognitive Decline
Authors: Mace Ryan A , Gates Melissa V , Bullard Breanna , Lester Ethan G , Silverman Ilyssa H , Quiroz Yakeel T , Vranceanu Ana-Maria 
Published: June 2020

AbstractBackground and ObjectivesChronic pain (CP) and cognitive decline (CD) often co-occur in older adults, which can reinforce a “disability spiral.” Early interventions teaching pain coping skills and gradual increases in activity (walking) are needed to promote overall well-being and potentially delay further decline of cognition and daily functioning. The goal of this mixed-methods study was to guide the development of two mind–body activity programs for CP and CD which focus on increasing walking using time goals (Active Brains) or step count reinforced by a Fitbit (Active Brains–Fitbit).Research Design and MethodsOlder adults with CP and CD (N = 23) participated in a one-time focus group (four total) and completed measures of physical, emotional, and cognitive functioning. Qualitative analyses identified population-specific needs, preferences, and perceptions of proposed program skills. Quantitative analysis compared clinical characteristics to population norms and explored intercorrelations among treatment targets.ResultsThematic analyses revealed six main themes: (1) challenges living with CP and (2) CD, (3) current walking, (4) technology (Fitbit) to increase walking, (5) perceptions of proposed program skills (e.g., mind–body, pain, and increased walking), and (6) program barriers and facilitators. Quantitative analyses showed that (a) participants had physical function below reference values and (b) higher self-efficacy correlated with higher cognitive, emotional, and physical functioning.Discussion and ImplicationsFocus group participants were enthusiastic about the proposed program skills. Current work includes open pilot testing, qualitative interviews, and a small randomized controlled trial to optimize the programs and methodology in preparation for efficacy testing against an educational control.