bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shift Work Sleep Disorder and Night Shift Work Significantly Impair Erectile Function
Authors: Rodriguez Katherine M. , Kohn Taylor P. , Kohn Jaden R. , Sigalos John T. , Kirby E. Will , Pickett Stephen M. , Pastuszak Alexander W. , Lipshultz Larry I. 
Published: July 2020

Abstract

Objectives
Here we examine the association between shift work sleep disorder (SWSD) and erectile dysfunction (ED) in shift workers.

Methods
Men presenting to a single andrology clinic between January 2014 and July 2017 completed validated questionnaires: International Index of Erectile Function (IIEF), Patient Health Questionnaire-9 (PHQ-9), and the nonvalidated SWSD Questionnaire. Men were also asked about shift work schedule, comorbidities, phosphodiesterase 5 (PDE5) inhibitor use, and testosterone use. Serum total testosterone values were determined for each visit. Linear regression was performed controlling for testosterone use, testosterone levels, PDE5 inhibitor use, age, and comorbidities to determine the effect of SWSD on ED as assessed using the IIEF.

Results
Of the 754 men completing questionnaires, 204 reported nonstandard shift work (begins before 7 am or after 6 pm, regularly extends out of that frame, or rotates frequently) and 48 were found to have SWSD using a screening questionnaire. Nonstandard shift work alone did not result in worse IIEF-EF scores (P = .31), but those who worked nonstandard shifts and had SWSD demonstrated IIEF-EF scores 2.8 points lower than men without SWSD (P &lt; .01). When assessing for the type of shift work performed, men who worked night shifts had IIEF-EF scores 7.6 points lower than men who worked during the day or evening (P &lt; .01). Testosterone use improved IIEF-EF scores for men with SWSD by 2.9 points, ameliorating the effect of SWSD on ED. However, baseline testosterone levels were not associated with worse erectile function in this cohort.

Conclusion
Men with SWSD have worse erectile function, with men who work night shifts having even poorer erectile function. These findings suggest that circadian rhythm disturbance may significantly impact erectile function. While testosterone therapy may partly reverse the effects of SWSD, shift work is a potential risk factor for ED and should be assessed for as part of the evaluation of men with ED.
Using the ArcGIS Collector Mobile App for Settlement Survey Data Collection in Armenia
Authors: Lindsay Ian , Kong Ningning Nicole 
Published: July 2020

AbstractRecent years have seen the rapid adoption of digital site recording strategies following the proliferation of GPS-enabled mobile devices and data collection apps. Much of the emerging literature on digital—or paperless—archaeology, however, has focused on excavation contexts, with fewer discussions of mobile-GIS solutions on archaeological survey. This article discusses the design and implementation of a site survey workflow based on Esri's ArcGIS Collector mobile app in the context of Project ArAGATS's Kasakh Valley Archaeology Survey in northwestern Armenia. The Collector app provides a simple, map-centric user interface that allows surveyors with little-to-no GIS experience to record site locations, enter attribute data on customized digital forms, and attach photographs. With a network connection, the Collector app instantly uploads site information as GIS data to the project geodatabase and refreshes the data across surveyors’ mobile devices. Although the Collector app lacks certain GIS features and requires an institutional Esri license, we found that the native integration with our project GIS and broad access to visualization and recording tools in the app made in-field decision-making and interpretation more collaborative and inclusive across the survey team.
The Philosophy of Accidentality
Authors: VARGAS MANUEL 
Published: July 2020

AbstractIn mid-twentieth-century Mexican philosophy, there was a peculiar nationalist existentialist project focused on the cultural conditions of agency. This article revisits some of those ideas, including the idea that there is an important but underappreciated experience of one's relationship to norms and social meanings. This experience—something called accidentality—casts new light on various forms of social subordination and socially scaffolded agency, including cultural alienation, biculturality, and double consciousness.
Feeding strategies and body condition of juvenile European flounderPlatichthys flesusin a nursery habitat
Authors: Mendes C. , Ramos S. , Elliott M. , Bordalo A. A. 
Published: July 2020

AbstractEstuarine habitats are major nurseries for the European flounderPlatichthys flesus, with different year classes sharing food and space resources. Hence, an understanding of feeding strategies that optimize resource use and maintain carrying capacity is fundamental for sustainable and successful ecosystem management. The main feeding areas of juvenile European flounder (including 0-group and 1-group age classes) in the Lima estuary (northern Portugal) nursery ground were investigated by integrating stomach content analyses with stable isotopic values (δ13C and δ15N) and fish condition indices (Fulton K and RNA:DNA ratio). The 0-group flounder that were associated with the upstream section of the estuary presented the lowest δ13C value (−25.58 ± 1.86‰), while 1-group flounder exhibited a higher δ13C value (−22.59 ± 2.51‰), indicating use of the more saline areas of the estuary (lower and middle sections). The two age groups did not differ in terms of δ15N (0-group: 13.93 ± 0.29‰; 1-group: 13.50 ± 0.96‰), indicating similar trophic levels. The low salinity upper estuary was the main feeding area of 0-group flounder (74%), while 1-group flounder fed along the estuary both upstream (52%) and downstream (48%). Juvenile flounder showed high individual condition based on the Fulton K index (0-group: 1.05 ± 0.08; 1-group: 1.07 ± 0.05) and RNA:DNA (0-group: 1.70 ± 0.70; 1-group: 1.41 ± 0.47). These indices deal with fish health, and hence indicate nursery habitat quality. It is concluded that in this temperate nursery habitat, different feeding strategies sustained the condition of the European flounder juveniles, compared with other flounder populations.
Essence, Explanation, and Modality
Authors: Wallner Michael , Vaidya Anand 
Published: July 2020

AbstractRecently, Kit Fine's (1994) view that modal truths aretrue in virtue of,grounded in, orexplained byessentialist truths has been under attack. In what follows we offer two responses to the wave of criticism against his view. While the first response is pretty straightforward, the second is based on the distinction between, what we call,Reductive Finean EssentialismandNon-Reductive Finean Essentialism. Engaging the work of Bob Hale onNon-Reductive Finean Essentialism, we aim to show that the arguments against Fine's view are unconvincing, while we acknowledge the presence of a deep standoff between the two views.
Generalized monoidal effects and handlers
Authors: PIETERS RUBEN P. , RIVAS EXEQUIEL , SCHRIJVERS TOM 
Published: July 2020

Abstract
Algebraic effects and handlers are a convenient method for structuring monadic effects with primitive effectful operations and separating the syntax from the interpretation of these operations. However, the scope of conventional handlers is limited as not all side effects are monadic in nature. This paper generalizes the notion of algebraic effects and handlers from monads to generalized monoids, which notably covers applicative functors and arrows as well as monads. For this purpose, we switch the category theoretical basis from free algebras to free monoids. In addition, we show how lax monoidal functors enable the reuse of handlers and programs across different computation classes, for example, handling applicative computations with monadic handlers. We motivate and present these handler interfaces in the context of build systems. Tasks in a build system are represented by a free computation and their interpretation as a handler. This use case is based on the work of Mokhov et al. [(2018). PACMPL2(ICFP), 79:1–79:29.].
Progressive right ventricular outflow tract fibrosis after repair of tetralogy of Fallot
Authors: Karur Gauri R. , Mawad Wadi , Grosse-Wortmann Lars 
Published: July 2020

AbstractObjectives:The objective of this study was to determine the evolution of fibrosis over time and its association with clinical status.Methods:Children with repaired tetralogy of Fallot who had undergone at least two cardiac magnetic resonance examinations including T1 mapping at least 1 year apart were included.Results:Thirty-seven patients (12.7 ± 2.6 years, 61% male) were included. Right ventricular free wall T1 increased (913 ± 208 versus 1023 ± 220 ms; p = 0.02). Baseline cardiac magnetic resonance parameters did not predict a change in imaging markers or exercise tolerance. The right ventricular free wall per cent change correlated with left ventricular T1% change (r = 0.51, p = 0.001) and right ventricular mass Z-score change (r = 0.51, p = 0.001). T1 in patients with late gadolinium enhancement did not differ from the rest.Conclusion:Increasing right ventricular free wall T1 indicates possible progressive fibrotic remodelling in the right ventricular outflow tract in this pilot study in children and adolescents with repaired tetralogy of Fallot. The value of T1 mapping both at baseline and during serial assessments will need to be investigated in larger cohorts with longer follow-up.
Vegetation Affects Timing and Location of Wetland Methane Emissions
Authors: Bansal Sheel , Johnson Olivia F. , Meier Jacob , Zhu Xiaoyan 
Published: July 2020

AbstractCommon assumptions about how vegetation affects wetland methane (CH4) flux include acting as conduits for CH4release, providing carbon substrates for growth and activity of methanogenic organisms, and supplying oxygen to support CH4oxidation. However, these effects may change through time, especially in seasonal wetlands that experience drying and rewetting, or change across space, dependent on proximity to vegetation. In a mesocosm study, we assessed the impacts ofTyphaon CH4flux using clear flux chamber measurements directly overTyphaplants (“whole‐plant”), adjacent toTyphaplants (where roots were present but no stems; “plant‐adjacent”), and plant‐free soils (“control”). During the establishment phase of the study (first 30 days), the whole‐plant treatment had ~5 times higher CH4flux rates (51.78 ± 8.16 mg‐C m−2day−1) than plant‐adjacent or control treatments, which was primarily due to plant‐mediated transport, with little contribution from diffusive‐only flux. However, porewater CH4concentrations were relatively low directly below whole‐plant and in neighboring plant‐adjacent treatments, while controls accumulated a highly concentrated reservoir of porewater CH4. When the water table was drawn down to simulate seasonal drying, reserve porewater CH4from control soil was released as a pulse, equaling the earlier higher CH4emissions from whole‐plants. Plant‐adjacent treatments, which had neither plant‐mediated CH4transport nor a concentrated reservoir of porewater CH4, had low CH4flux throughout the study. Our findings indicate that in seasonal wetlands, vegetation affects the timing and location of CH4emissions. These results have important mechanistic and methodological implications for understanding the role of vegetation on wetland CH4flux.
Association between adjuvant chemotherapy and survival in patients with rectal cancer and pathological complete response after neoadjuvant chemoradiotherapy and resection
Authors: He Fang , Ju Huai-Qiang , Ding Yi , Jiang Zhiqiang , Li Zhenhui , Huang Bo , Wang Xiuhong , Zhao Yuanyuan , Li Yong , Qi Bin , Luo Wenguang , Zhang Zijian , Pei Qian , Chen Haiyang , Liu Shuai , Pang Xiaolin , Zheng Jian , Wang Jianping , Ajani Jaffer A. , Wan Xiang-Bo 
Published: July 2020

Abstract
Background
For patients with locally advanced rectal cancer (LARC), it is unclear whether neoadjuvant chemoradiotherapy-induced pathologic complete response (pCR) individuals would further benefit from adjuvant chemotherapy (ACT).

Methods
The pCR individuals who received different ACT cycles were paired by propensity score matching. Overall survival (OS), disease-free survival (DFS), local recurrence-free survival (LRFS), and distant metastasis-free survival (DMFS) were calculated by Kaplan–Meier and log-rank test.

Results
In total, 1041 pCR individuals were identified from 5567 LARC cases. Specifically, 303 pCR cases had no ACT treatment, and 738 pCR patients received fluoropyrimidine-based ACT (median, 4 cycles) treatment. After 1:3 propensity score matching, 297 cases without ACT treatment were matched to 712 cases who received ACT treatment. Kaplan–Meier analysis showed that pCR individuals treated with or without ACT had the similar 3-year outcome (OS, DFS, LRFS and DMFS) (all P > 0.05). Moreover, the pCR patients received different ACT cycle(s) (0 vs. 1–4 cycles, 0 vs. ≥5 cycles) had comparable 3-year OS, DFS, LRFS and DMFS (all P > 0.05). In stratified analysis, ACT treatment did not improve 3-year survival (OS, DFS, LRFS and DMFS) for the baseline high-risk (cT3–4/cN1–2) subgroup patients (all P > 0.05).

Conclusion
ACT, which did not improve survival, is unnecessary to neoadjuvant treatment-induced pCR LARC patients.

Trial registration
2019ZSLYEC-136 (24-6-2019).
Contributions of de novo variants to systemic lupus erythematosus
Authors: Almlöf Jonas Carlsson , Nystedt Sara , Mechtidou Aikaterini , Leonard Dag , Eloranta Maija-Leena , Grosso Giorgia , Sjöwall Christopher , Bengtsson Anders A. , Jönsen Andreas , Gunnarsson Iva , Svenungsson Elisabet , Rönnblom Lars , Sandling Johanna K. , Syvänen Ann-Christine 
Published: July 2020

AbstractBy performing whole-genome sequencing in a Swedish cohort of 71 parent-offspring trios, in which the child in each family is affected by systemic lupus erythematosus (SLE, OMIM 152700), we investigated the contribution of de novo variants to risk of SLE. We found de novo single nucleotide variants (SNVs) to be significantly enriched in gene promoters in SLE patients compared with healthy controls at a level corresponding to 26 de novo promoter SNVs more in each patient than expected. We identified 12 de novo SNVs in promoter regions of genes that have been previously implicated in SLE, or that have functions that could be of relevance to SLE. Furthermore, we detected three missense de novo SNVs, five de novo insertion-deletions, and three de novo structural variants with potential to affect the expression of genes that are relevant for SLE. Based on enrichment analysis, disease-affecting de novo SNVs are expected to occur in one-third of SLE patients. This study shows that de novo variants in promoters commonly contribute to the genetic risk of SLE. The fact that de novo SNVs in SLE were enriched to promoter regions highlights the importance of using whole-genome sequencing for identification of de novo variants.
A crop type dataset for consistent land cover classification in Central Asia
Authors: Remelgado Ruben , Zaitov Sherzod , Kenjabaev Shavkat , Stulina Galina , Sultanov Murod , Ibrakhimov Mirzakhayot , Akhmedov Mustakim , Dukhovny Victor , Conrad Christopher 
Published: July 2020

AbstractLand cover is a key variable in the context of climate change. In particular, crop type information is essential to understand the spatial distribution of water usage and anticipate the risk of water scarcity and the consequent danger of food insecurity. This applies to arid regions such as the Aral Sea Basin (ASB), Central Asia, where agriculture relies heavily on irrigation. Here, remote sensing is valuable to map crop types, but its quality depends on consistent ground-truth data. Yet, in the ASB, such data are missing. Addressing this issue, we collected thousands of polygons on crop types, 97.7% of which in Uzbekistan and the remaining in Tajikistan. We collected 8,196 samples between 2015 and 2018, 213 in 2011 and 26 in 2008. Our data compile samples for 40 crop types and is dominated by “cotton” (40%) and “wheat”, (25%). These data were meticulously validated using expert knowledge and remote sensing data and relied on transferable, open-source workflows that will assure the consistency of future sampling campaigns.
The structural basis of the genetic code: amino acid recognition by aminoacyl-tRNA synthetases
Authors: Kaiser Florian , Krautwurst Sarah , Salentin Sebastian , Haupt V. Joachim , Leberecht Christoph , Bittrich Sebastian , Labudde Dirk , Schroeder Michael 
Published: July 2020

AbstractStorage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. We extensively characterize how these enzymes distinguish all natural amino acids based on the computational analysis of crystallographic structure data. The results of this meta-analysis show that the correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric effects.
Climate smart Dry Chain Technology for safe storage of quinoa seeds
Authors: Bakhtavar Muhammad Amir , Afzal Irfan 
Published: July 2020

AbstractQuinoa (Chenopodium quinoa) is a climate resilient crop having superior nutritional profile compared to other cereal grains and may help to ensure future food security. Commercial cultivation of quinoa is dependent upon availability of quality seed. Adoption of Dry Chain Technology: drying before storage and maintaining seed dryness through hermetic packaging, may prevent quinoa seed deterioration. Quinoa seeds were dried to 8, 10, 12 and 14% initial seed moisture content (SMC) and stored in conventional (Paper, polypropylene, cloth and jute) and hermetic Super Bags for 6, 12 and 18 months. Seed stored in Super Bag at 8% initial SMC maintained low seed moisture and higher germination. Total soluble sugars and α-amylase activity were higher while EC, reducing sugars and MDA contents were low for the seeds stored in hermetic bag at 8% initial SMC. Seed stored in traditional packaging materials irrespective of initial seed moisture contents, gained moisture due to ambient high relative humidity which resulted in seed deterioration as indicated by increased reducing sugars, MDA contents and seed leachates conductivity and reduced vigor, viability, soluble sugars. The Dry Chain Technology preserves seed quality by maintaining low seed moisture and reducing deteriorative physiological and biochemical changes in the quinoa seed.
Narrow genetic base shapes population structure and linkage disequilibrium in an industrial oilseed crop, Brassica carinata A. Braun
Authors: Khedikar Yogendra , Clarke Wayne E. , Chen Lifeng , Higgins Erin E. , Kagale Sateesh , Koh Chu Shin , Bennett Rick , Parkin Isobel A. P. 
Published: July 2020

AbstractEthiopian mustard (Brassica carinataA. Braun) is an emerging sustainable source of vegetable oil, in particular for the biofuel industry. The present study exploited genome assemblies of the Brassica diploids,Brassica nigraandBrassica oleracea,to discover over 10,000 genome-wide SNPs using genotype by sequencing of 620B. carinatalines. The analyses revealed a SNP frequency of one every 91.7 kb, a heterozygosity level of 0.30, nucleotide diversity levels of 1.31 × 10−05, and the first five principal components captured only 13% molecular variation, indicating low levels of genetic diversity among theB. carinatacollection. Genome bias was observed, with greater SNP density found on the B subgenome. The 620 lines clustered into two distinct sub-populations (SP1 and SP2) with the majority of accessions (88%) clustered in SP1 with those from Ethiopia, the presumed centre of origin. SP2 was distinguished by a collection of breeding lines, implicating targeted selection in creating population structure. Two selective sweep regions on B3 and B8 were detected, which harbour genes involved in fatty acid and aliphatic glucosinolate biosynthesis, respectively. The assessment of genetic diversity, population structure, and LD in the globalB. carinatacollection provides critical information to assist future crop improvement.
Anti-biofilm efficacy of a medieval treatment for bacterial infection requires the combination of multiple ingredients
Authors: Furner-Pardoe Jessica , Anonye Blessing O. , Cain Ricky , Moat John , Ortori Catherine A. , Lee Christina , Barrett David A. , Corre Christophe , Harrison Freya 
Published: July 2020

AbstractNovel antimicrobials are urgently needed to combat drug-resistant bacteria and to overcome the inherent difficulties in treating biofilm-associated infections. Studying plants and other natural materials used in historical infection remedies may enable further discoveries to help fill the antibiotic discovery gap. We previously reconstructed a 1,000-year-old remedy containing onion, garlic, wine, and bile salts, known as ‘Bald’s eyesalve’, and showed it had promising antibacterial activity. In this current paper, we have found this bactericidal activity extends to a range of Gram-negative and Gram-positive wound pathogens in planktonic culture and, crucially, that this activity is maintained against Acinetobacter baumannii, Stenotrophomonas maltophilia, Staphylococcus aureus, Staphylococcus epidermidis and Streptococcus pyogenes in a soft-tissue wound biofilm model. While the presence of garlic in the mixture can explain the activity against planktonic cultures, garlic has no activity against biofilms. We have found the potent anti-biofilm activity of Bald’s eyesalve cannot be attributed to a single ingredient and requires the combination of all ingredients to achieve full activity. Our work highlights the need to explore not only single compounds but also mixtures of natural products for treating biofilm infections and underlines the importance of working with biofilm models when exploring natural products for the anti-biofilm pipeline.
BDNF belongs to the nurse-like cell secretome and supports survival of B chronic lymphocytic leukemia cells
Authors: Talbot Hugo , Saada Sofiane , Barthout Elodie , Gallet Paul-François , Gachard Nathalie , Abraham Julie , Jaccard Arnaud , Troutaud Danielle , Lalloué Fabrice , Naves Thomas , Fauchais Anne-Laure , Jauberteau Marie-Odile 
Published: July 2020

AbstractEvading apoptosis and sustained survival signaling pathways are two central hallmarks of B-cell chronic lymphocytic leukemia (B-CLL) cells. In this regard, nurse-like cells (NLC), the monocyte-derived type 2 macrophages, deliver stimulatory signals via B-cell activating factor (BAFF), a proliferation-inducing ligand (APRIL), and the C-X-C Motif Chemokine Ligand 12 (CXCL12). Previously, we demonstrated that brain-derived neurotrophic factor (BDNF) protects B-CLL cells from spontaneous apoptosis by activating the oncogenic complex NTSR2-TrkB (neurotensin receptor 2-tropomyosin-related kinase receptor B), only overexpressed in B-CLL cells, inducing anti-apoptotic protein Bcl-2 (B-cell lymphoma 2) expression and Src kinase survival signaling pathways. Herein, we demonstrate that BDNF belongs to the NLC secretome and promotes B-CLL survival. This was demonstrated in primary B-CLL co-cultured with their autologous NLC, compared to B-CLL cells cultured alone. Inhibition of BDNF in co-cultures, enhances B-CLL apoptosis, whereas its exogenous recombinant activates pro-survival pathways in B-CLL cultured alone (i.e. Src activation and Bcl-2 expression), at a higher level than those obtained by the exogenous recombinant cytokines BAFF, APRIL and CXCL12, the known pro-survival cytokines secreted by NLC. Together, these results showed that BDNF release from NLC trigger B-CLL survival. Blocking BDNF would support research strategies against pro-survival cytokines to limit sustained B-CLL cell survival.