bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fish can save energy via proprioceptive sensing
Authors: Li Liang , Liu Danshi , Deng Jian , Lutz Matthew J , Xie Guangming 
Published: July 2021

Abstract
Fish have evolved diverse and robust locomotive strategies to swim efficiently in complex fluid environments. However, we know little, if anything, about how these strategies can be achieved. Although most studies suggest that fish rely on the lateral line system to sense local flow and optimise body undulation, recent work has shown that fish are still able to gain benefits from the local flow even with the lateral line impaired. In this paper, we hypothesise that fish can save energy by extracting vortices shed from their neighbours using only simple proprioceptive sensing with the caudal fin. We tested this hypothesis on both computational and robotic fish by synthesising a central pattern generator (CPG) with feedback, proprioceptive sensing, and reinforcement learning. The CPG controller adjusts the body undulation after receiving feedback from the proprioceptive sensing signal, decoded via reinforcement learning. In our study, we consider potential proprioceptive sensing inputs to consist of low-dimensional signals (e.g. perceived forces) detected from the flow. With simulations on a computational robot and experiments on a robotic fish swimming in unknown dynamic flows, we show that the simple proprioceptive sensing is sufficient to optimise the body undulation to save energy, without any input from the lateral line. Our results reveal a new sensory-motor mechanism in schooling fish and shed new light on the strategy of control for robotic fish swimming in complex flows with high efficiency.
The impacts of special environmental events on short-run electricity-saving behaviors
Authors: Shen Xingchi , Qiu Yueming , Luo Ling , Zheng Xiaohao 
Published: July 2021

Abstract
Policymakers and academics are increasingly interested in using ‘social nudges’ to influence behavior, which are typically inexpensive relative to price-based and mandatory approaches. This study provides rigorous empirical evidence of the impacts of three big special environmental events, as a specific form of nudge, on short-run electricity-saving behaviors using high-frequency smart meter data in Shanghai, China, for both residential and commercial consumers. We find that World Environment Day and National Energy Saving Publicity Week caused commercial users to reduce their electricity consumption by 1.35 kWh h−1 and 0.6 kWh h−1 intra-event, around 17% and 8% reduction compared to average consumption, but the impacts decayed rapidly once the events ended. Earth Hour did not lead to significant energy-saving effects for both residential and commercial users. We further examine detailed activities implemented during these events to understand the heterogeneous impacts using social media and policy documents data.
Recent changes in cropland area and productivity indicate unsustainable cropland expansion in Malawi
Authors: Li Chengxiu , Kandel Matt , Anghileri Daniela , Oloo Francis , Kambombe Oscar , Chibarabada Tendai Polite , Ngongondo Cosmo , Sheffield Justin , Dash Jadunandan 
Published: July 2021

Abstract
Cropland expansion is a common strategy for boosting agricultural production in sub-Saharan Africa (SSA) even though it often leads to economic, environmental, and social trade-offs. Ensuring sustainable cropland use and their management is critical for improving food security and preserving ecosystem services. To develop policies and approaches that support sustainable cropland management at national and sub-national scales, there is a need to understand the spatial distribution of cropland expansion (/loss), and any resultant changes in cropland productivity. This is especially important in SSA countries such as Malawi, where spatially explicit assessments of changes in cropland area and cropland productivity are lacking. To address this gap in Malawi, we used multi-source satellite data and socio-economic data, combined with satellite image classification and trend analysis, firstly to quantify spatial changes in cropland area and productivity, and secondly to evaluate potentially available cropland for future expansion. We found evidence of unsustainable cropland use in Malawi, which was demonstrated by: (a) rapid cropland expansion between 2010 and 2019 (increase 8.5% of land area), characterized by an expansion of crop farming into upland areas which indicate increased land scarcity in Malawi; (b) limited potential for future expansion, as approximately only 5% of the total land remained as potentially available cropland (corresponding to 4671 000 ha); and (c) an overall reduction in cropland productivity and a prevalence of increase in soil erosion. Our findings underscore the urgent need for taking measures to promote sustainable cropland use, including by protecting current cropland from further degradation (e.g. Southern Malawi) and improving cropland use planning (e.g. Northern Malawi).
Continuously spacing-tunable multi-wavelength single-frequency fiber laser based on cascaded four-wave mixing at 1.06 μm
Authors: Teng Xiaodan , Yang Changsheng , Guo Yuankai , Ma Pengfei , Lin Wei , Guan Xianchao , Tan Tianyi , Zhao Qilai , Feng Zhouming , Wei Xiaoming , Xu Shanhui 
Published: July 2021

Abstract
A continuously spacing-tunable multi-wavelength single-frequency fiber laser (MW-SFFL) at 1.06 μm is investigated based on cascaded four-wave mixing (CFWM) in a high-nonlinearity photonic crystal fiber (HN-PCF). By using two separate wavelength-tunable continuous-wave (CW) SFFLs for pumping the HN-PCF, the MW-SFFL with up to ten stable wavelengths is generated under a total pump power of 890 mW. Furthermore, when the wavelength and the power of pump lasers are appropriately manipulated, the wavelength spaces of the MW-SFFL can be tuned freely within 166 pm and the numbers of wavelengths can be controlled to 4, 6, 8, and 10, respectively. To our knowledge, it is demonstrated for the first time that the MW-SFFL based on CFWM at 1.0 μm band are directly excited by CW SFFLs.
Flat band properties of twisted transition metal dichalcogenide homo- and heterobilayers of MoS2, MoSe2, WS2 and WSe2
Authors: Vitale V , Atalar K , Mostofi A A , Lischner J 
Published: July 2021

Abstract
Twisted bilayers of two-dimensional materials, such as twisted bilayer graphene, often feature flat electronic bands that enable the observation of electron correlation effects. In this work, we study the electronic structure of twisted transition metal dichalcogenide homo- and heterobilayers that are obtained by combining MoS2, WS2, MoSe2 and WSe2 monolayers, and show how flat band properties depend on the chemical composition of the bilayer as well as its twist angle. We determine the relaxed atomic structure of the twisted bilayers using classical force fields and calculate the electronic band structure using a tight-binding model parametrized from first-principles density-functional theory. We find that the highest valence bands in these systems can derive either from Γ-point or K/

K

′

-point states of the constituent monolayers. For homobilayers, the two highest valence bands are composed of monolayer Γ-point states, exhibit a graphene-like dispersion and become flat as the twist angle is reduced. The situation is more complicated for heterobilayers where the ordering of Γ-derived and K/

K

′

-derived states depends both on the material composition and also the twist angle. In all systems, qualitatively different band structures are obtained when atomic relaxations are neglected.
Pharmacist intervention on prescribing errors: Use of a standardized approach in the inpatient setting
Authors: Cabri Ann , Barsegyan Naira , Postelnick Michael , Schulz Lucas , Nguyen Victoria , Szwak Jennifer , Shane Rita 
Published: July 2021

AbstractPurposeThe objective of this study was to implement a standardized process across health systems to determine the prevalence and clinical relevance of prescribing errors intercepted by pharmacists.MethodsThis prospective, multicenter, observational study was conducted across 11 hospitals. Pharmacist-intercepted prescribing errors were collected during inpatient order verification over 6 consecutive weeks utilizing a standardized documentation process. The potential harm of each error was evaluated using a modified National Coordinating Council for Medication Error Reporting and Prevention (NCC-MERP) index with physician validation, and errors were stratified into those with potentially low, serious, or life-threatening harm. Endpoints included the median error rate per 1,000 patient days, error type, and potential harm with correlating cost avoidance.ResultsPharmacists intervened on 7,187 errors, resulting in a mean error rate of 39 errors per 1,000 patient days. Among the errors, 46.6% (n = 3,349) were determined to have potentially serious consequences and 2.4% (n = 175) could have been life-threatening if not intercepted. This equates to $874,000 in avoided cost. The top 3 error types occurring with the highest frequency were “wrong dose/rate/frequency” (n = 2,298, 32.0%), “duplicate therapy” (n = 1,431, 19.9%), and “wrong timing” (n = 960, 13.4%). “Wrong dose/rate/frequency” (n = 49, 28%), “duplicate therapy” (n = 26, 14.9%), and “drug-disease interaction” (n = 24, 13.7%) errors occurred with the highest frequency among errors with potential for life-threatening harm. “Wrong dose/rate/frequency” (n = 1,028, 30.7%), “wrong timing” (n = 573, 17.1%), and “duplicate therapy” (n = 482, 14.4%) errors occurred with the highest frequency among errors with potentially serious harm.ConclusionDocumentation of pharmacist intervention on prescribing errors via a standardized process creates a platform for multicenter analysis of prescribing error trends and an opportunity for development of system-wide solutions to reduce potential harm from prescribing errors.
Evaluation of discharge prescribing after rescheduling of gabapentin as a controlled substance
Authors: Robbins Melody J , Floroff Catherine , Ingemi Amanda , Kaplan Marcus C 
Published: July 2021

Abstract

Purpose
Gabapentin has increasingly been identified as a drug of abuse, especially when used concurrently with opioids. Rescheduling gabapentin as a Schedule V controlled substance may strengthen monitoring and prescribing restrictions. The purpose of this study was to characterize the impact of rescheduling gabapentin from a nonscheduled to a Schedule V substance in Virginia on discharge prescribing patterns in a health system.

Methods
This was a retrospective, pre-post, multicenter chart review conducted at 4 sites. Data from 3 months before gabapentin rescheduling (prerescheduling group) and 3 months after gabapentin rescheduling (postrescheduling group) were evaluated. The primary outcome was the percentage of newly prescribed gabapentin prescriptions upon discharge, which was compared between the pre- and postrescheduling groups.

Results
A similar percentage of gabapentin prescriptions were newly prescribed in the prerescheduling group as compared to the postrescheduling group (55.0% vs 50.0%, P = 0.479). Gabapentin prescribing characteristics did not differ between the groups for new gabapentin prescriptions (n = 55 in the prerescheduling group, n = 50 in the postrescheduling group). Concomitant discharge prescribing of benzodiazepines (5.5% vs 2.0%, P = 0.619) and opioids (45.5% vs 60.0%, P = 0.136) did not differ significantly between the postrescheduling group and prerescheduling group for new gabapentin prescriptions. However, fewer opioid prescriptions exceeded 90 daily morphine milligram equivalents (MME) in the postrescheduling group as compared to the prerescheduling group for new gabapentin prescriptions (36.0% vs 20.0%, P = 0.020).

Conclusion
Gabapentin prescribing practices did not differ before and after rescheduling of gabapentin as a controlled substance. There was a trend toward dosages with reduced daily MME for concomitant opioid prescriptions after rescheduling. However, additional investigation with larger studies over longer periods of time is needed to discover whether gabapentin rescheduling significantly changes prescribing practices.
Loneliness and Daily Alcohol Consumption During the COVID-19 Pandemic
Authors: Bragard Elise , Giorgi Salvatore , Juneau Paul , Curtis Brenda L 
Published: July 2021

Abstract

Aims
This pilot study aimed to identify associations of loneliness and daily alcohol consumption among US adults during the Coronavirus Disease-2019 pandemic.

Method
Participants completed daily assessments for 30 days.

Results
Results suggest people who feel lonelier on average drink more alcohol, however, people who feel lonelier than usual drink less.

Conclusion
Findings highlight the need to disaggregate within- and between-person components of alcohol use.
Negotiations over parental care: a test of alternative hypotheses in the clown anemonefish
Authors: Barbasch Tina A , Branconi Rebecca , Francis Robin , Pacaro Madison , Srinivasan Maya , Jones Geoffrey P , Buston Peter M 
Published: July 2021

Abstract
In species with biparental care, conflict arises over how much each parent provides to their offspring because both parents benefit from shifting the burden of care to the other. Here, we tested alternative hypotheses for how parents will negotiate offspring care using a wild population of clownfish (Amphiprion percula). We experimentally handicapped parents by fin-clipping the female in 23 groups, the male in 23 groups, and neither parent in 23 groups and measured changes in indicators of female, male, and pair effort in response to handicapping. First, we found that handicapping resulted in a decrease in the number of eggs laid by fin-clipped females and a decrease in the amount of parental care by fin-clipped males. Second, contrary to predictions, female effort did not change in response to the male being handicapped, or vice versa. Finally, the number of embryos that matured to hatching, an indicator of pair effort, was not influenced by the manipulation, suggesting that although the handicap was effective, clownfish do not face the predicted “cost to conflict” when one parent is handicapped. Together, these results test the generality of theoretical predictions and uncover novel questions about whether and how negotiations operate in systems where interests are aligned.
A fast data-driven method for genotype imputation, phasing and local ancestry inference: MendelImpute.jl
Authors: Chu Benjamin B , Sobel Eric M , Wasiolek Rory , Ko Seyoon , Sinsheimer Janet S , Zhou Hua , Lange Kenneth 
Published: July 2021

Abstract

Motivation
Current methods for genotype imputation and phasing exploit the volume of data in haplotype reference panels and rely on hidden Markov models (HMMs). Existing programs all have essentially the same imputation accuracy, are computationally intensive and generally require prephasing the typed markers.

Results
We introduce a novel data-mining method for genotype imputation and phasing that substitutes highly efficient linear algebra routines for HMM calculations. This strategy, embodied in our Julia program MendelImpute.jl, avoids explicit assumptions about recombination and population structure while delivering similar prediction accuracy, better memory usage and an order of magnitude or better run-times compared to the fastest competing method. MendelImpute operates on both dosage data and unphased genotype data and simultaneously imputes missing genotypes and phase at both the typed and untyped SNPs (single nucleotide polymorphisms). Finally, MendelImpute naturally extends to global and local ancestry estimation and lends itself to new strategies for data compression and hence faster data transport and sharing.

Availability and implementation
Software, documentation and scripts to reproduce our results are available from https://github.com/OpenMendel/MendelImpute.jl.

Supplementary information
Supplementary data are available at Bioinformatics online.
Accurate spliced alignment of long RNA sequencing reads
Authors: Sahlin Kristoffer , Mäkinen Veli 
Published: July 2021

Abstract

Motivation
Long-read RNA sequencing technologies are establishing themselves as the primary techniques to detect novel isoforms, and many such analyses are dependent on read alignments. However, the error rate and sequencing length of the reads create new challenges for accurately aligning them, particularly around small exons.

Results
We present an alignment method uLTRA for long RNA sequencing reads based on a novel two-pass collinear chaining algorithm. We show that uLTRA produces higher accuracy over state-of-the-art aligners with substantially higher accuracy for small exons on simulated and synthetic data. On simulated data, uLTRA achieves an accuracy of about 60% for exons of length 10 nucleotides or smaller and close to 90% accuracy for exons of length between 11 and 20 nucleotides. On biological data where true read location is unknown, we show several examples where uLTRA aligns to known and novel isoforms containing small exons that are not detected with other aligners. While uLTRA obtains its accuracy using annotations, it can also be used as a wrapper around minimap2 to align reads outside annotated regions.

Availabilityand implementation
uLTRA is available at https://github.com/ksahlin/ultra.

Supplementary information
Supplementary data are available at Bioinformatics online.
Destroying and Restoring Critical Habitats of Endangered Killer Whales
Authors: Williams Rob , Ashe Erin , Broadhurst Ginny , Jasny Michael , Tuytel Dyna , Venton Margot , Ragen Tim 
Published: July 2021

Abstract
Endangered species legislation in the United States and Canada aims to prevent extinction of species, in part by designating and protecting critical habitats essential to ensure survival and recovery. These strict laws prohibit adverse modification or destruction of critical habitat, respectively. Defining thresholds for such effects is challenging, especially for wholly aquatic taxa. Destruction of critical habitat (e.g., prey reduction and ocean noise) threatens the survival and recovery of the 75 members of the endangered southern resident killer whale population found in transboundary (Canada–United States) Pacific waters. The population's dynamics are now driven largely by the cumulative effects of prey limitation (e.g., the endangered Chinook salmon), anthropogenic noise and disturbance (e.g., reducing prey accessibility), and toxic contaminants, which are all forms of habitat degradation. It is difficult to define a single threshold beyond which habitat degradation becomes destruction, but multiple lines of evidence suggest that line may have been crossed already.
Chest X-ray Analysis With Deep Learning-Based Software as a Triage Test for Pulmonary Tuberculosis: An Individual Patient Data Meta-Analysis of Diagnostic Accuracy
Authors: Tavaziva Gamuchirai , Harris Miriam , Abidi Syed K , Geric Coralie , Breuninger Marianne , Dheda Keertan , Esmail Aliasgar , Muyoyeta Monde , Reither Klaus , Majidulla Arman , Khan Aamir J , Campbell Jonathon R , David Pierre-Marie , Denkinger Claudia , Miller Cecily , Nathavitharana Ruvandhi , Pai Madhukar , Benedetti Andrea , Ahmad Khan Faiz 
Published: July 2021

Abstract

Background
Automated radiologic analysis using computer-aided detection software (CAD) could facilitate chest X-ray (CXR) use in tuberculosis diagnosis. There is little to no evidence on the accuracy of commercially available deep learning-based CAD in different populations, including patients with smear-negative tuberculosis and people living with human immunodeficiency virus (HIV, PLWH).

Methods
We collected CXRs and individual patient data (IPD) from studies evaluating CAD in patients self-referring for tuberculosis symptoms with culture or nucleic acid amplification testing as the reference. We reanalyzed CXRs with three CAD programs (CAD4TB version (v) 6, Lunit v3.1.0.0, and qXR v2). We estimated sensitivity and specificity within each study and pooled using IPD meta-analysis. We used multivariable meta-regression to identify characteristics modifying accuracy.

Results
We included CXRs and IPD of 3727/3967 participants from 4/7 eligible studies. 17% (621/3727) were PLWH. 17% (645/3727) had microbiologically confirmed tuberculosis. Despite using the same threshold score for classifying CXR in every study, sensitivity and specificity varied from study to study. The software had similar unadjusted accuracy (at 90% pooled sensitivity, pooled specificities were: CAD4TBv6, 56.9% [95% confidence interval {CI}: 51.7–61.9]; Lunit, 54.1% [95% CI: 44.6–63.3]; qXRv2, 60.5% [95% CI: 51.7–68.6]). Adjusted absolute differences in pooled sensitivity between PLWH and HIV-uninfected participants were: CAD4TBv6, −13.4% [−21.1, −6.9]; Lunit, +2.2% [−3.6, +6.3]; qXRv2: −13.4% [−21.5, −6.6]; between smear-negative and smear-positive tuberculosis was: were CAD4TBv6, −12.3% [−19.5, −6.1]; Lunit, −17.2% [−24.6, −10.5]; qXRv2, −16.6% [−24.4, −9.9]. Accuracy was similar to human readers.

Conclusions
For CAD CXR analysis to be implemented as a high-sensitivity tuberculosis rule-out test, users will need threshold scores identified from their own patient populations and stratified by HIV and smear status.
Therapeutic siRNAs Targeting the JAK/STAT Signalling Pathway in Inflammatory Bowel Diseases
Authors: Clément Flora , Nougarède Adrien , Combe Stéphanie , Kermarrec Frédérique , Dey Arindam K , Obeid Patricia , Millet Arnaud , Navarro Fabrice P , Marche Patrice N , Sulpice Eric , Gidrol Xavier 
Published: July 2021

Abstract

Background and Aims
Inflammatory bowel diseases are highly debilitating conditions that require constant monitoring and life-long medication. Current treatments are focused on systemic administration of immunomodulatory drugs, but they have a broad range of undesirable side-effects. RNA interference is a highly specific endogenous mechanism that regulates the expression of the gene at the transcript level, which can be repurposed using exogenous short interfering RNA [siRNA] to repress expression of the target gene. While siRNA therapeutics can offer an alternative to existing therapies, with a high specificity critical for chronically administrated drugs, evidence of their potency compared to chemical kinase inhibitors used in clinics is still lacking in alleviating an adverse inflammatory response.

Methods
We provide a framework to select highly specific siRNA, with a focus on two kinases strongly involved in pro-inflammatory diseases, namely JAK1 and JAK3. Using western-blot, real-time quantitative PCR and large-scale analysis, we assessed the specificity profile of these siRNA drugs and compared their efficacy to the most recent and promising kinase inhibitors for Janus kinases [Jakinibs], tofacitinib and filgotinib.

Results
siRNA drugs can reach higher efficiency and selectivity at lower doses [5 pM vs 1 µM] than Jakinibs. Moreover, JAK silencing lasted up to 11 days, even with 6 h pulse transfection.

Conclusions
The siRNA-based drugs developed hold the potential to develop more potent therapeutics for chronic inflammatory diseases.