bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Syringe Service Program Within a Federal System
Authors: Lynch Rebecca D. , Biederman Donna J. , Silva Susan , Demasi Kim 
Published: May 2021

Abstract

Background
Drug use, specifically opioid use, is a public health crisis in the United States. Harm reduction programs, including syringe service programs, show efficacy in improving individual and public health outcomes. Healthcare provider perceptions are an important initial assessment when considering implementing a syringe service program.

Objective
The objective of this quality improvement project, completed in a Northeastern Veterans Affairs Medical Center (NEVAMC), was to lay the groundwork for implementation of a syringe service program.

Methods
This multiphase project included an initial needs assessment with stakeholders to determine the scope of substance use disorder within the facility and initiated the change process needed for syringe service program implementation. We administered an online survey, the Drug and Drug Problems Perceptions Questionnaire (DDPPQ), to better understand staff perspectives of and comfort in working with people who use drugs. Two educational modules were developed and conducted for staff to increase their knowledge, skills, and trauma-informed practices when working with people who use drugs. Standardized document templates for program implementation in federal systems were also developed.

Results
The needs assessment identified 266 patients who could benefit from expanded harm reduction services and a recognition that staff perception be assessed within the facility. The DDPPQ, completed by 153 staff members, indicated positive perceptions of people who use drugs and ability to counsel/treat people who use drugs. The median DDPPQ total score was 73, indicative of an overall positive perception. Sixty-eight staff members attended the initial education session, and 35 attended the second session designed specifically for mental health service line professionals.

Conclusion
The findings indicate NEVAMC staff members have a high level of comfort working with people who use drugs. The staff educational programs were well received and have become a part of routine staff training at the NEVAMC. The standardized document templates are available for persons developing a syringe service program within a federal system.
Implementing Clinical Practice Guidelines for Tobacco Cessation in a Women's Residential Substance Use Treatment Facility
Authors: Madden Brandee J. , Fogger Susanne A. 
Published: May 2021

Abstract

Background
Tobacco is the leading cause of preventable death, and over 200,000 women die each year of diseases caused by tobacco. Women with substance use disorders (SUDs) are disproportionately affected. Smoking prevalence among individuals enrolled in SUD treatment is 2–4 times higher than that of the general population, yet less than half of all treatment facilities offer tobacco treatment services. However, when individuals combine treatment, they have a greater likelihood of long-term abstinence from alcohol and other substances of use.

Methods
A quality improvement project was undertaken to implement the U.S. Public Health Service guideline for tobacco cessation in a women's residential substance use treatment facility. Tobacco users were advised on their health risk and recommended to cut down or quit. They were advised that help was available using nicotine replacement therapy, behavioral counseling, or both.

Results
Upon admission, 67% of clients received brief advice to quit, and 30% participated in an intensive treatment aimed at reducing or eliminating cigarette use. At discharge, counseling participants (n = 21) smoked an average of nine cigarettes per day, reduced from 23, which was statistically significant.

Implications for Practice
Interventions reduced cigarette smoking in a population at a high risk for adverse outcomes related to use. Results suggest that more clients are interested in tobacco treatment than previously estimated. Increased administrative, clinical, and pharmacy support can sustain and further assist clients with cessation efforts.
Presacral Ewing's sarcoma mimicking piriformis syndrome
Authors: Liu Kuan-Fu , Chou Chen-Liang , Liu Ding-Hao 
Published: May 2021

Abstract

Rationale:
Piriformis syndrome is caused by entrapment or irritation of the sciatic nerve through a tight or hypertrophic piriformis muscle. Patients usually have buttock pain with sciatica. However, clinical management of piriformis syndrome is still challenging and results in repetitive investigations with potentially misleading diagnoses

Patient concerns:
This was a case of a thirty-six-year-old young woman, who suffered from progressive sciatica on and off for nine months. However, the symptoms progressed under conservative treatment.

Diagnoses:
Piriformis syndrome was diagnosed at first. Ultrasound-guided anesthetic injection over the piriformis muscle was performed, with no alleviation of symptoms. Then Magnetic Resonance Imaging revealed a space-occupying lesion over the presacral region, which was further confirmed by tissue biopsy as Ewing's sarcoma of the sacrum with right S1 and S2 nerve root compression.

Interventions:
The patient received neoadjuvant chemotherapy and tumor excision surgery.

Outcomes:
The patient was followed-up for 15 months with non-progression of residual tumor and complete resolution of sciatica.

Lessons:
Patients with sciatica should be evaluated by history taking and careful physical examination, followed by serial neurophysiological and imaging studies. To manage unresponsive piriformis syndrome, imaging studies should cover the pelvic and hip areas to assess the deep gluteal and pelvic region, because tumors compressing sciatic nerve can mimic piriformis syndrome. This case report aims at raising clinical awareness of the complexity of sciatica and piriformis syndrome.
Correction of the Deepened Labiomental Groove Using Silicone Implants in Advancement Genioplasty
Authors: Hwang Jungil , Park Bumjin 
Published: May 2021

Abstract
Advancement genioplasty is performed to aesthetically improve the lower third of the facial profile. Excessive chin advancement alone may lead to deepened labiomental sulcus and deformed aesthetic results. The purpose of this study was to assess the efficacy of silicone prosthesis placement as an alternative method for effacing an excessively deepened labiomental groove after advancement genioplasty. Three hundred and seventy-six patients underwent genioplasty between January 2014 and October 2017. Among these were 216 cases of advancement genioplasty, of which 79 (62 females and 17 males) underwent advancement procedures using silicone implants. Inserting the silicone implant at the sulcus easily removes the deepened groove. This procedure could be an easy and reliable method for attaining an aesthetically pleasing result in excessive advancement genioplasty.
Effectiveness of BNT162b2 and mRNA-1273 COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe COVID-19 outcomes in Ontario, Canada: a test-negative design study
Authors: Chung Hannah , He Siyi , Nasreen Sharifa , Sundaram Maria E. , Buchan Sarah A. , Wilson Sarah E. , Chen Branson , Calzavara Andrew , Fell Deshayne B. , Austin Peter C. , Wilson Kumanan , Schwartz Kevin L. , Brown Kevin A. , Gubbay Jonathan B. , Basta Nicole E. , Mahmud Salaheddin M. , Righolt Christiaan H. , Svenson Lawrence W. , MacDonald Shannon E. , Janjua Naveed Z. , Tadrous Mina , Kwong Jeffrey C. 
Published: May 2021

ABSTRACTObjectivesTo estimate the effectiveness of mRNA COVID-19 vaccines against symptomatic infection and severe outcomes.DesignWe applied a test-negative design study to linked laboratory, vaccination, and health administrative databases, and used multivariable logistic regression adjusting for demographic and clinical characteristics associated with SARS-CoV-2 and vaccine receipt to estimate vaccine effectiveness (VE) against symptomatic infection and severe outcomes.SettingOntario, Canada between 14 December 2020 and 19 April 2021.ParticipantsCommunity-dwelling adults aged ≥16 years who had COVID-19 symptoms and were tested for SARS-CoV-2.InterventionsPfizer-BioNTech’s BNT162b2 or Moderna’s mRNA-1273 vaccine.Main outcome measuresLaboratory-confirmed SARS-CoV-2 by RT-PCR; hospitalization/death associated with SARS-CoV-2 infection.ResultsAmong 324,033 symptomatic individuals, 53,270 (16.4%) were positive for SARS-CoV-2 and 21,272 (6.6%) received ≥1 vaccine dose. Among test-positive cases, 2,479 (4.7%) had a severe outcome. VE against symptomatic infection ≥14 days after receiving only 1 dose was 60% (95%CI, 57 to 64%), increasing from 48% (95%CI, 41 to 54%) at 14–20 days after the first dose to 71% (95%CI, 63 to 78%) at 35–41 days. VE ≥7 days after 2 doses was 91% (95%CI, 89 to 93%). Against severe outcomes, VE ≥14 days after 1 dose was 70% (95%CI, 60 to 77%), increasing from 62% (95%CI, 44 to 75%) at 14–20 days to 91% (95%CI, 73 to 97%) at ≥35 days, whereas VE ≥7 days after 2 doses was 98% (95%CI, 88 to 100%). For adults aged ≥70 years, VE estimates were lower for intervals shortly after receiving 1 dose, but were comparable to younger adults for all intervals after 28 days. After 2 doses, we observed high VE against E484K-positive variants.ConclusionsTwo doses of mRNA COVID-19 vaccines are highly effective against symptomatic infection and severe outcomes. Single-dose effectiveness is lower, particularly for older adults shortly after the first dose.
DeepNull: Modeling non-linear covariate effects improves phenotype prediction and association power
Authors: McCaw Zachary R. , Colthurst Thomas , Yun Taedong , Furlotte Nicholas A. , Carroll Andrew , Alipanahi Babak , McLean Cory Y. , Hormozdiari Farhad 
Published: May 2021

AbstractGenome-wide association studies (GWAS) examine the association between genotype and phenotype while adjusting for a set of covariates. Although the covariates may have non-linear or interactive effects, due to the challenge of specifying the model, GWAS often neglect such terms. Here we introduce DeepNull, a method that identifies and adjusts for non-linear and interactive covariate effects using a deep neural network. In analyses of simulated and real data, we demonstrate that DeepNull maintains tight control of the type I error while increasing statistical power by up to 20% in the presence of non-linear and interactive effects. Moreover, in the absence of such effects, DeepNull incurs no loss of power. When applied to 10 phenotypes from the UK Biobank (n=370K), DeepNull discovered more hits (+6%) and loci (+7%), on average, than conventional association analyses, many of which are biologically plausible or have previously been reported. Finally, DeepNull improves upon linear modeling for phenotypic prediction (+23% on average).
The sensory and motor components of the cortical hierarchy are coupled to the rhythm of the stomach during rest
Authors: Rebollo Ignacio , Tallon-Baudry Catherine 
Published: May 2021

AbstractBodily rhythms appear as novel scaffolding mechanisms orchestrating the spatio-temporal organization of spontaneous brain activity. Here, we follow up on the discovery of the gastric resting-state network (Rebollo et al, 2018), composed of brain regions in which the fMRI signal is phase-synchronized to the slow (0.05 Hz) electrical rhythm of the stomach. Using a larger sample size (n=63 human participants), we further characterize the anatomy and effect sizes of gastric-brain coupling across resting-state networks, a fine grained cortical parcellation, as well as along the main gradients of cortical organization. Most (67%) of the gastric network is included in the somato-motor-auditory (38%) and visual (29%) resting state networks. Gastric brain coupling also occurs in the granular insula and, to a lesser extent, in the piriform cortex. Thus, all sensory and motor cortices corresponding to both exteroceptive and interoceptive modalities are coupled to the gastric rhythm during rest. Conversely, little gastric-brain coupling occurs in cognitive networks and transmodal regions. These results suggest not only that gastric rhythm and sensory-motor processes are likely to interact, but also that gastric-brain coupling might be a mechanism of sensory and motor integration that mostly bypasses cognition, complementing the classical hierarchical organization of the human brain.Significance statementWhile there is growing interest for brain-body communication in general and brain-viscera communication in particular, little is known about how the brain interacts with the gastric rhythm, the slow electrical rhythm continuously produced in the stomach. Here, we show in human participants at rest that the gastric network, composed of brain regions synchronized with delays to the gastric rhythm, includes all motor and sensory (vision, audition, touch and interoception, olfaction) regions, but only few of the transmodal regions associated with higher-level cognition. Such results prompt for a reconsideration of the classical view of cortical organization, where the different sensory modalities are considered as relatively independent modules.
Crossing design shapes patterns of genetic variation in synthetic recombinant populations ofSaccharomyces cerevisiae
Authors: Phillips Mark A. , Kutch Ian C. , McHugh Kaitlin M. , Taggard Savannah K. , Burke Molly K. 
Published: May 2021

Abstract“Synthetic recombinant” populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinantSaccharomyces cerevisiaepopulations created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.
Machine learning-enabled cancer diagnostics with widefield polarimetric second-harmonic generation microscopy
Authors: Mirsanaye Kamdin , Castaño Leonardo Uribe , Kamaliddin Yasmeen , Golaraei Ahmad , Augulis Renaldas , Kontenis Lukas , Done Susan J. , Žurauskas Edvardas , Wilson Brian C. , Barzda Virginijus 
Published: May 2021

AbstractThe extracellular matrix (ECM) collagen undergoes major remodeling during tumorigenesis. However, alterations to the ECM are not widely considered in cancer diagnostics, due to mostly uniform appearance of collagen fibers in white light images of hematoxylin and eosin-stained tissue sections. Polarimetric second-harmonic generation (P-SHG) microscopy enables label-free visualization and ultrastructural investigation of non-centrosymmetric molecules, which, when combined with texture analysis, provides multiparameter characterization of tissue collagen. This paper demonstrates whole slide imaging of breast tissue microarrays using high-throughput widefield P-SHG microscopy. The resulting P-SHG parameters are used in classification to differentiate tumor tissue from normal with 94.2% accuracy and F1-score, and 6.3% false discovery rate. Subsequently, the trained classifier is employed to predict tumor tissue with 91.3% accuracy, 90.7% F1-score, and 13.8% false omission rate. As such, we show that widefield P-SHG microscopy reveals collagen ultrastructure over large tissue regions and can be utilized as a sensitive biomarker for cancer diagnostics and prognostics studies.
Effect of straw incorporation and nitrification inhibitor on nitrous oxide emission in various cropland soils and its microbial mechanism
Authors: Zhang Ya-Bo , Liu Feng , Wang Jun-Tao , Hu Hang-Wei , He Ji-Zheng , Zhang Li-Mei 
Published: May 2021

AbstractNitrification inhibitor and straw incorporation are widely used to improve crop nitrogen use efficiency in agricultural soil, but their effects on nitrous oxide (N2O) emission across different soil types and the microbial mechanisms remain less understood. In this study, we used controlled experiment and DNA-based molecular analysis to study how nitrification inhibitor (dicyandiamide, DCD) and straw incorporation affect soil nitrogen balance, N2O emission and microbial nitrifiers/denitrifers in three distinct agricultural soils (the black, fluvo-aquic and red soils) across China. Both DCD and straw incorporation improved nitrogen balance by increasing NH4+ and decreasing NO3- in all soils. DCD tended to decrease N2O emission from all soils especially the fluvo-aquic one, while straw incorporation reduced N2O emission only in the fluvo-aquic soil but increased N2O emission in the other two especially the red soil (by ∼600%). T-RFLP analysis revealed that the denitriers community structure are distinct among the three soils but was not strongly affected by DCD or straw incorporation. qPCR analysis revealed that DCD or straw incorporation had no significant effect on nitrifier abundance but increased nitrous oxide reductase nosZ gene abundance in the black/fluvo-aquic soil rather than the red soil. Structural equational modelling further confirmed that, when accounting for treatments and soil properties, nosZ gene abundance is the only biological factor significantly determined N2O emission in different soil types. Taken together, our work advanced the knowledge on the agricultural practices and N2O emission in cropland soils, suggesting that straw incorporation may not be a good choice for the red and black soil areas; management practices should be used as per soil type to balance between nitrogen use efficiency and N2O emission.
Functional connectome reorganization relates to post-stroke motor recovery and structural disruption
Authors: Olafson Emily R , Jamison Keith W , Sweeney Elizabeth M , Liu Hesheng , Wang Danhong , Bruss Joel E , Boes Aaron D , Kuceyeski Amy 
Published: May 2021

AbstractMotor recovery following ischemic stroke is contingent on the ability of surviving brain networks to compensate for damaged tissue. In rodent models, sensory and motor cortical representations have been shown to remap onto intact tissue around the lesion site, but remapping to more distal sites (e.g. in the contralesional hemisphere) has also been observed. Resting state functional connectivity (FC) analysis has been employed to study compensatory network adaptations in humans, but mechanisms and time course of motor recovery are not well understood. Here, we examine longitudinal FC in 23 first-episode ischemic pontine stroke patients (34-74 years old; 8 female, 15 male) and utilize a graph matching approach to identify patterns of regional functional connectivity reorganization during recovery. We quantified functional reorganization between several intervals ranging from 1 week to 6 months following stroke, and demonstrated that the areas that undergo functional reorganization most frequently are in cerebellar/subcortical networks. Brain regions with more structural connectome disruption due to the stroke also had more functional remapping over time. Finally, we show that the amount of functional reorganization between time points is correlated with the extent of motor recovery observed between those time points in the early to late subacute phases, and, furthermore, individuals with greater baseline motor impairment demonstrate more extensive early subacute functional reorganization (from one to two weeks post-stroke) and this reorganization correlates with better motor recovery at 6 months. Taken together, these results suggest that our graph matching approach can quantify recovery-relevant, whole-brain functional connectivity network reorganization after stroke.
Jasmine: Population-scale structural variant comparison and analysis
Authors: Kirsche Melanie , Prabhu Gautam , Sherman Rachel , Ni Bohan , Aganezov Sergey , Schatz Michael C. 
Published: May 2021

AbstractThe increasing availability of long-reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine (https://github.com/mkirsche/Jasmine), a fast and accurate method for SV refinement, comparison, and population analysis. Using an SV proximity graph, Jasmine outperforms five widely-used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than five-fold, and reveals a set of high confidence de novo SVs confirmed by multiple long-read technologies. We also present a harmonized callset of 205,192 SVs from 31 samples of diverse ancestry sequenced with long reads. We genotype these SVs in 444 short read samples from the 1000 Genomes Project with both DNA and RNA sequencing data and assess their widespread impact on gene expression, including within several medically relevant genes.
A generic systems-theoretic approach to identify biological networks capable of adaptation
Authors: Bhattacharya Priyan , Raman Karthik , Tangirala Arun K. 
Published: May 2021

AbstractConstructing biological networks capable of performing specific biological functionalities has been of sustained interest in synthetic biology. Adaptation is one such ubiquitous functional property, which enables every living organism to sense a change in its surroundings and return to its operating condition prior to the disturbance. In this paper, we present a generic systems theory-driven method for designing adaptive protein networks. First, we translate the necessary qualitative conditions for adaptation to mathematical constraints using the language of systems theory, which we then map back as ‘design requirements’ for the underlying networks. We go on to prove that a protein network with different input–output nodes (proteins) needs to be at least of third-order in order to provide adaptation. Next, we show that the necessary design principles obtained for a three-node network in adaptation consist of negative feedback or a feed-forward realization. Interestingly, the design principles obtained by the proposed method remain the same for a network of arbitrary size and connectivity. Finally, we prove that the motifs discovered for adaptation are non-retroactive for a canonical downstream connection. This result explains how complex biological networks achieve robustness while keeping the core motifs unchanged in the context of a particular functionality. We corroborate our theoretical results with detailed and thorough numerical simulations. Overall, our results present a generic, systematic and robust framework for designing various kinds of biological networks.
Electrolysis of Bacterial Biofilm
Authors: Bazargani Abdollah , Azimi Arsalan , Farhadi Pouya , Irvani Seyed Sina Naghibi , Moatari Psalm 
Published: May 2021

AbstractBiofilms are a significant global health problem and are of most important clinical impediments of the century. Biofilms play a crucial role in antimicrobial resistance and chronic infections by acting as reservoir for microorganisms. Therefore greater understanding of biofilm and novel methods to eliminate them are needed. We considered electrolysis as a contrivance to decompose and disperse thePseudomonas aeruginosa biofilmin microtiter dishes. We showed electrolysis effectively eliminated thePseudomonas aeruginosa biofilm with the potential to change our approach in tackling biofilms.