bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel approach for estimating growth and mortality of fish larvae
Authors: Hinchliffe Charles , Pepin Pierre , Suthers Iain M , Falster Daniel S 
Published: August 2021

Abstract
Accurate estimates of growth and mortality are needed to understand drivers of production and cohort success. Existing methods for estimating mortality rates, such as catch-curves, require large sample sizes, as they work by grouping individuals into age-bins to determine a frequency distribution. Yet, sampling enough larvae is often not possible at fine scales within the constraints of research projects, due to low density of larvae in pelagic environments. Here, we develop a novel method to simultaneously estimate growth and mortality rates of fish larvae as a continuous function of size using theory of size-structured populations, eliminating the need to group data into age-bins. We compare the effectiveness of our model to existing methods by generating data from a known distribution. This comparison demonstrates that while all models recover correct parameter values under ideal circumstances, our new method performs better than existing methods when sample sizes are low. Additionally, our method can accommodate non-linear growth and mortality functions, while also allowing growth and mortality to vary as functions of environmental co-variates. This increased accuracy and flexibility of our method should improve our ability to relate variability in larval production to environmental fluctuations at finer spatial scales.
Extended set of solutions of a bounded finite-time stabilization problem via the controllability function
Authors: Choque-Rivero A E 
Published: August 2021

Abstract
For the two-dimensional canonical system, an extended set of bounded finite-time stabilizing positional controls is proposed. For the construction of such controls, which depend on a certain parameter, the Korobov’s controllability function method is used. Such an extension is based on the enlarging of the interval of the mentioned parameter, as well as the use of the non-uniqueness of the controllability function for some regions of the phase space ${\mathbb R}^2.$ Additionally, we characterize a region of initial conditions $x^0$ on ${\mathbb R}^2$ of the given system for which the time of motion from $x^0$ to the origin is less than the value of the controllability function.
Characterization of recombinant murine GDE4 and GDE7, enzymes producing lysophosphatidic acid and/or cyclic phosphatidic acid
Authors: Tserendavga Binderiya , Ohshima Noriyasu , Fujita Chiaki , Yuzawa Koji , Ohshima Mari , Yanaka Noriyuki , Minamishima Yoji Andrew , Izumi Takashi 
Published: August 2021

Abstract
GDE4 and GDE7 are membrane-bound enzymes that exhibit lysophospholipase D activities. We found that GDE7 produced not only lysophosphatidic acid (LPA) but also cyclic phosphatidic acid (cPA) from lysophospholipids by a transphosphatidylation reaction. In contrast, GDE4 produced only LPA. The analysis of substrate specificity showed that 1-alkyl-lysophosphospholipids were preferred substrates for both enzymes rather than 1-alkyl-lysophospholipids and 1-alkenyl-lysophospholipids. Among the various lysophospholipids with different polar head groups that were tested, lysophosphatidylglycerol and lysophosphatidylserine were preferred substrates for GDE4 and GDE7, respectively. The detailed analysis of the dependency of the enzyme activities of GDE4 and GDE7 on divalent cations suggested multiple divalent cations were bound in the active sites of both enzymes. Taken together, these results suggest the possibility that GDE7 functions as a cPA-producing enzyme in the body.
Fracture analysis for materials by a stable generalized/extended finite element method
Authors: Jia H G , Zhao Y M , Nie Y F , Li S Q 
Published: August 2021

ABSTRACT
In this paper, a method is proposed for extracting fracture parameters in isotropic material cracking via a stable generalized/extended finite element method. The numerical results of the stress intensity factors and scaled condition number of the system matrix are presented and compared with different enrichment schemes or those reported in related references. The good agreement and convergence of the results obtained by the developed method with those obtained by other solutions or enrichment schemes proves the applicability of the proposed approach and confirms its capability of efficiently extracting fracture parameters in isotropic materials.
Pb/Bi heterostructure as a versatile platform to realize topological superconductivity
Authors: Watanabe Ikuko , Souma Seigo , Nakayama Kosuke , Sugawara Katsuaki , Trang Chi Xuan , Segawa Kouji , Yamauchi Kunihiko , Oguchi Tamio , Takahashi Takashi , Sato Takafumi 
Published: August 2021

Abstract
Realization of topological superconductors (TSCs) hosting Majorana fermions is an exciting challenge in materials science. Majorana fermions are predicted to emerge at vortex cores of two-dimensional (2D) TSCs and at both ends of one-dimensional (1D) TSCs; these two types of TSCs have been explored independently in different materials. Here, a system which has a potential to access both 1D and 2D TSCs in a single platform, Pb(111)/Bi(111) heterostructure, is proposed. One to twenty bilayers (BLs) of Bi(111) ultra-thin films are epitaxially fabricated on TlBiSe$_2$, and an intriguing evolution of electronic states upon variation of Bi-layer thickness is revealed by angle-resolved photoemission spectroscopy. The metallic quantum-well states at 1–2BLs are found to turn into the Rashba states at 5–20BLs, via the semiconducting states at 3BL. Fabrication of a Pb(111) film on 20BL Bi(111) enables observation of the proximity-induced superconductivity in Bi(111) as evident from a 1 meV energy gap at 5 K; these energy and temperature scales are considerably larger than those of Rashba superconductors. The Pb/Bi heterostructure serves as a versatile platform to study the interplay among proximity-induced superconductivity, band structure, and topology.
Complete Genome Sequence Data of Four Burkholderia glumae Strains Isolated from Rice Fields in the United States
Authors: Lee Hyun-Hee , Lelis Tiago , Ontoy John , Bruno Jobelle , Ham Jong Hyun , Seo Young-Su 
Published: August 2021

Bacterial panicle blight caused by Burkholderia glumae is a major disease in rice production worldwide. Currently, only a few whole-genome sequences of B. glumae strains isolated in the United States are available. Here, we report the complete genome sequence of four B. glumae strains, including three virulent strains (336gr-1, 411gr-6, and 957856-41-c) and the nonpathogenic strain B. glumae 257sh-1, which were isolated from rice fields in Louisiana (336gr-1, 957856-41-c, and 257sh-1) and Arkansas (411gr-6). The whole-genome sequence data of B. glumae strains will contribute to investigations of the molecular mechanism underlying bacterial pathogenicity and virulence to rice plants. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Characterization of Biopsies by Dermatologists and Nonphysician Providers in the Medicare Population: A Rapidly Changing Landscape
Authors: Patel Shreya , Nguyen Bichchau T. 
Published: August 2021

BACKGROUND
Previous studies show that nonphysician providers may require a higher number of biopsies to identify skin malignancies than dermatologists. Therefore, understanding the trends behind the types of providers performing biopsies may help analyze their impact on this vulnerable population.

OBJECTIVE
This retrospective study analyzes changes in nationwide, regional, and state-level data on the number and proportion of biopsies performed by dermatologists compared with nonphysician providers.

MATERIALS AND METHODS
Biopsy cases were isolated in the Medicare database from 2012 to 2018 using the HCPCS codes 11,100 and 11,101. Cases were limited to biopsies performed by a dermatologist, nurse practitioner (NP), or physician assistant (PA).

RESULTS
From 2012 to 2018, national biopsy rates per 100,000 Medicare beneficiaries for dermatologists decreased by 6%, whereas those for NPs and PAs increased by 97% and 82%, respectively. Each state showed variation in both the proportion of biopsies by provider type and the net change in biopsies rates over time. All states saw increases in the number of biopsies per 100,000 Medicare beneficiaries by nonphysician providers.

CONCLUSION
As the number of Medicare beneficiaries continues to grow, nonphysician providers are performing an increasing proportion of biopsies, with specific states and regions being affected more than others.
Histologic Comparison of Upper Blepharoplasty Skin Excision Using Scalpel Incision Versus Microdissection Electrocautery Needle Tip Versus Continuous Wave CO2 Laser
Authors: Carqueville Jordan C. , Chesnut Cameron 
Published: August 2021

BACKGROUND
The various techniques of upper blepharoplasty have been compared based on surgical time to perform the procedure, postoperative healing, scar cosmesis, and cost. Few studies have evaluated the histology of the excised tissue, and no study has compared the tissue histology of 3 blepharoplasty methods using scalpel, microdissection needle with electrocautery, and CO2 laser excision in the same patient.

OBJECTIVE
To evaluate the histologic changes of tissue after removal of upper eyelid skin using scalpel incision, microdissection electrocautery needle, and CO2 laser.

METHODS
Upper blepharoplasty skin excisions were examined from specimens obtained using scalpel incision, microdissection needle tip with electrocautery, and CO2 continuous wave beam. The specimens were sent for permanent sections for histologic evaluation.

RESULTS
The skin that was removed using cold steel scalpel incision showed no cellular necrosis or heat artifact. The tissue treated with the CO2 laser demonstrated significant thermal injury, including loss of cellular polarity, keratinocyte necrosis, and separation of the epidermis from the basement membrane. The skin excised using the electrocautery microdissection needle demonstrated fulguration artifact, including spindling of the epidermal nuclei with palisading of the keratinocytes. Necrosis was not prominent in the electrocautery microdissection needle specimens.

CONCLUSION
The amount of histologic tissue injury was greatest in the skin treated with continuous wave CO2 laser, followed by the microdissection needle with electrocautery. The cold steel scalpel incision showed no cellular necrosis.
Dissecting neuropathic from poststroke pain: the white matter within
Authors: Delboni Lemos Marcelo , Faillenot Isabelle , Tavares Lucato Leandro , Jacobsen Teixeira Manoel , Mendonça Barbosa Luciana , Joaquim Lopes Alho Eduardo , Bastos Conforto Adriana , Lilian de Lima Rodrigues Antonia , Galhardoni Ricardo , Aparecida da Silva Valquíria , Listik Clarice , Rosi Jefferson , Peyron Roland , Garcia-Larrea Luis , Ciampi de Andrade Daniel 
Published: August 2021

Abstract
Poststroke pain (PSP) is a heterogeneous term encompassing both central neuropathic (ie, central poststroke pain [CPSP]) and nonneuropathic poststroke pain (CNNP) syndromes. Central poststroke pain is classically related to damage in the lateral brainstem, posterior thalamus, and parietoinsular areas, whereas the role of white matter connecting these structures is frequently ignored. In addition, the relationship between stroke topography and CNNP is not completely understood. In this study, we address these issues comparing stroke location in a CPSP group of 35 patients with 2 control groups: 27 patients with CNNP and 27 patients with stroke without pain. Brain MRI images were analyzed by 2 complementary approaches: an exploratory analysis using voxel-wise lesion symptom mapping, to detect significant voxels damaged in CPSP across the whole brain, and a hypothesis-driven, region of interest–based analysis, to replicate previously reported sites involved in CPSP. Odds ratio maps were also calculated to demonstrate the risk for CPSP in each damaged voxel. Our exploratory analysis showed that, besides known thalamic and parietoinsular areas, significant voxels carrying a high risk for CPSP were located in the white matter encompassing thalamoinsular connections (one-tailed threshold Z > 3.96, corrected P value <0.05, odds ratio = 39.7). These results show that the interruption of thalamocortical white matter connections is an important component of CPSP, which is in contrast with findings from nonneuropathic PSP and from strokes without pain. These data can aid in the selection of patients at risk to develop CPSP who could be candidates to pre-emptive or therapeutic interventions.
Trends in the Utilization and Dose of Gabapentinoids in Combination With Opioids in an Injured Worker Population Between 2008 and 2018
Authors: Lavin Robert A. , Liu Che , Yuspeh Larry , Kalia Nimisha , Leung Nina , Tsourmas Nicholas F. , Williams Leila , Hunt Dan L. , Bernacki Edward J. , Tao Xuguang (Grant) 
Published: August 2021

Objective:
To determine long term (11 year) trends in gabapentin and pregabalin prescribing among workers’ compensation claimants at various opioid dose combinations (low, medium, high, and very high) in Louisiana.

Method:
A longitudinal study of 18,737 claimants who filled any prescriptions between 2008 and 2018.

Results:
The proportion of claimants prescribed opioids alone at all dose levels decreased dramatically. The proportion claimants prescribed the combination of low dose opioids and low dose gabapentinoids increased (7.7% to 10.9%). Prescribing higher daily doses of gabapentinoids was associated with higher daily doses of opioids. Gabapentinoid prescribing was associated with continued prescribing of medium and high dose opioids as claims matured.

Conclusions:
Overall opioid prescribing decreased over time, while prescribing low dose opioids with gabapentinoids, increased.
Prevalence of Untreated HIV and Associated Risk Behaviors Among the Sexual Partners of Recent Migrants and Long-term Residents in Rakai, Uganda
Authors: Brophy Jennifer E. , Lessler Justin , Ssekubugu Robert , Kennedy Caitlin E. , Chang Larry W. , Kigozi Godfrey , Ndyanabo Anthony , Kigozi Grace , Nalugoda Fred , Gray Ronald H. , Wawer Maria J. , Serwadda David M. , Reynolds Steven J. , Kagaayi Joseph , Grabowski Mary K. 
Published: August 2021

Background:
Migrants in sub-Saharan Africa are at increased risk of HIV acquisition after migration, but little is known about their sexual partners at place of destination.

Setting:
Rakai Community Cohort Study (RCCS) in Uganda.

Methods:
From 1999 to 2016, persons aged 15–49 years were surveyed in the RCCS and reported on their 4 most recent sexual partners in the last year. We compared the characteristics of sexual partners reported by migrants moving into RCCS communities in the last 2 years (ie, in-migrants) with those of long-term residents with no recent migration history. Among a subset of participants in cohabitating epidemiologically linked couples of known HIV serostatus, we also assessed prevalence of having ≥1 untreated HIV-positive partner among in-migrants and long-term residents.

Results:
One hundred sixteen thousand seven hundred forty-four sexual partners were reported by 29,423 participants. The sexual partnerships of in-migrants were significantly less likely to be marital, more likely to span community boundaries, and shorter in duration than those of long-term residents. In-migrants also reported more sexual partners and were less likely to know their partner's HIV status or to have told their partner their HIV status. Among 7558 epidemiologically linked couples, HIV-negative in-migrants were more likely to partner with untreated HIV-positive persons compared with HIV-negative long-term residents (women: 6.3% vs. 4.1%; prevalence risk ratio = 1.77, 95% confidence interval: 1.49 to 2.11; men: 6.9% vs. 3.9%; prevalence risk ratio = 1.72, 95% confidence interval: 1.38–2.14).

Conclusion:
There is a higher frequency of risky sexual behaviors among the partnerships of in-migrants compared with those of long-term residents. Among cohabitating couples, in-migrants are more likely to partner with untreated HIV-positive individuals.
Total Neoadjuvant Therapy Versus Standard Neoadjuvant Chemoradiation in Patients with Locally Advanced Rectal Cancer
Authors: Goffredo Paolo , Khan Adil , Mott Sarah L. , Jensen Christine C. , Madoff Robert D. , Gaertner Wolfgang B. , You Y. Nancy , Hassan Imran 
Published: August 2021

Objective:
To evaluate the impact of neoadjuvant multi-agent systemic chemotherapy and radiation (TNT) vs neoadjuvant single-agent chemoradiation (nCRT) and multi-agent adjuvant chemotherapy on overall survival (OS), tumor downstaging, and circumferential resection margin (CRM) status in patients with locally advanced rectal cancer.

Summary of Background Data:
Outside of clinical trials and small institutional reports, there is a paucity of data regarding the short and long-term oncologic impact of TNT as compared to nCRT.

Methods:
Adult patients with stage II-III rectal adenocarcinoma were identified in the National Cancer Database [2006–2015].

Results:
Out of 8,548 patients, 36% received TNT and 64% nCRT. In the cohort, 13% had a pCR and 20% a neoadjuvant rectal (NAR) score <8. In multivariable analysis, as compared to nCRT, TNT demonstrated numerically higher pCR rates (P = 0.05) but had similar incidence of positive CRM (P = 0.11). Similar results were observed with NAR scores <8 as the primary endpoint. After adjusting for confounders, OS was comparable between the 2 groups. Additional factors independently associated with lower OS included male gender, uninsured status, low income status, high comorbidity score, poorly differentiated tumors, abdominoperineal resection, and positive surgical margins (all P <0.01). In separate models, both pCR and a NAR score <8 were associated with improved OS.

Conclusion:
In this national cohort, TNT was not associated with better survival and/or CRM negative status in comparison with nCRT, despite numerically higher downstaging rates. Further refinement of patient selection and treatment regimens are needed to establish effective neoadjuvant platforms to improve outcomes of patients with rectal cancer.
Dual Versus Single Oxygenated Hypothermic Machine Perfusion of Porcine Livers: Impact on Hepatobiliary and Endothelial Cell Injury
Authors: de Vries Yvonne , Brüggenwirth Isabel M. A. , Karangwa Shanice A. , von Meijenfeldt Fien A. , van Leeuwen Otto B. , Burlage Laura C. , de Jong Iris E. M. , Gouw Annette S. H. , de Meijer Vincent E. , Lisman Ton , Porte Robert J. 
Published: August 2021

Background.
Hypothermic oxygenated machine perfusion (HOPE) reduces ischemia-reperfusion injury of donor livers and is increasingly used in clinical transplantation. However, it remains unclear whether perfusion via the portal vein alone (HOPE) or via both the portal vein and hepatic artery (dual HOPE or DHOPE) is superior.

Methods.
Twelve porcine livers donated after circulatory death were randomized for 2 h of HOPE (n = 6) or DHOPE (n = 6), followed by 4 h of warm reperfusion with whole blood, to mimic transplantation. Hepatobiliary and endothelial cell function and injury markers were determined in perfusate and bile samples. Biopsies of bile ducts, hepatic arteries, and liver parenchyma were collected to assess histological damage and the expression of endothelial protective genes (KLF-2, eNOS, ET-1, CD31, VWF, VEGF-A).

Results.
There were no differences in hepatobiliary function and injury after warm reperfusion between the groups, apart from a 2-fold lower concentration of alanine aminotransferase in the perfusate (P = 0.045) and a lower peak lactate dehydrogenase in bile (P = 0.04) of livers preserved by DHOPE. Endothelial cell function and injury, as assessed by perfusate nitric oxide and von Willebrand factor antigen levels, as well as endothelial protective gene expressions, were similar between the groups. The hepatic arteries of both groups showed no microscopic evidence of injury.

Conclusions.
This study did not reveal major differences in hepatobiliary or endothelial function and injury after preservation by single or dual HOPE of porcine livers donated after circulatory death.
Development and Preliminary Evaluation of a Patient-facing Educational Video About Live Kidney Donor Surgical Complications
Authors: Smith Sophia , Haseley Nicole , Keller Maria , Cadzow Renee , Feeley Thomas H. , Kayler Liise K. 
Published: August 2021

Background.
Living kidney donation (LKD) improves transplant access; however, its use is compromised, in part, by individuals’ unaddressed concerns about perioperative complications.

Methods.
We developed an animated, patient-centered educational video about LKD surgical complications, with input from experts in transplantation, communication, and anthropology, 35 patients/care partners (5 LKD candidates, 5 prior LKDs, 10 kidney transplant recipients, 10 kidney transplant candidates, 5 care partners), and 1 community advocate. We then conducted an online pre-post study with 24 potential kidney donors and recipients to measure the video’s acceptability and feasibility to improve donation complication knowledge and concerns.

Results.
Knowledge of LKD surgical complications increased 23% (mean 5.7 to 7.0, P < 0.01) from pre- to post- animation viewing. Large knowledge effect size increases were observed for different levels of age, race, health literacy, and technology access. The frequency of positive responses about donation safety increased from 88% preanimation to 96% postanimation. Concerns about surgical complications remained at 17% before and after exposure. After viewing the animation, over 90% indicated positive ratings on ease of watching, understanding, and engaging.

Conclusions.
An animated educational video about LKD surgical complications was developed in collaboration with multiple stakeholders. The video was well received and promised to positively impact individuals’ knowledge and concerns.
Ion-dependent structure, dynamics, and allosteric coupling in a non-selective cation channel
Authors: Lewis Adam , Kurauskas Vilius , Tonelli Marco , Henzler-Wildman Katherine 
Published: August 2021

ABSTRACTThe selectivity filter (SF) determines which ions are efficiently conducted through ion channel pores. NaK is a non-selective cation channel that conducts Na+ and K+ with equal efficiency. Crystal structures of NaK suggested a rigid SF structure, but later solid-state NMR and MD simulations questioned this interpretation. Here, we use solution NMR to characterize how bound Na+ vs. K+ affects NaK SF structure and dynamics. We find that the extracellular end of the SF is flexible on the ps-ns timescale regardless of bound ion. On a slower timescale, we observe a structural change between the Na+ and K+-bound states, accompanied by increased structural heterogeneity in Na+. We also show direct evidence that the SF structure is communicated to the pore via I88 on the M2 helix. These results support a dynamic SF with multiple conformations involved in non-selective conduction. Our data also demonstrate allosteric coupling between the SF and pore-lining helices in a non-selective cation channel that is analogous to the allosteric coupling previously demonstrated for K+-selective channels, supporting the generality of this model.