bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can Minimally Invasive Esophagectomy Replace Open Esophagectomy for Esophageal Cancer? Latest Analysis of 24,233 Esophagectomies From the Japanese National Clinical Database
Authors: Yoshida Naoya , Yamamoto Hiroyuki , Baba Hideo , Miyata Hiroaki , Watanabe Masayuki , Toh Yasushi , Matsubara Hisahiro , Kakeji Yoshihiro , Seto Yasuyuki 
Published: February 2019

Objective:
We aimed to elucidate whether minimally invasive esophagectomy (MIE) can be safely performed by reviewing the Japanese National Clinical Database.

Summary of Background Data:
MIE is being increasingly adopted, even for advanced esophageal cancer that requires various preoperative treatments. However, the superiority of MIE's short-term outcomes compared with those of open esophagectomy (OE) has not been definitively established in general clinical practice.

Methods:
This study included 24,233 esophagectomies for esophageal cancer conducted between 2012 and 2016. Esophagectomy for clinical T4 and M1 stages, urgent esophagectomy, 2-stage esophagectomy, and R2 resection were excluded. The effects of preoperative treatment and surgery on short-term outcomes were analyzed using generalized estimating equations logistic regression analysis.

Results:
MIE was superior or equivalent to OE in terms of the incidence of most postoperative morbidities and surgery-related mortality, regardless of the type of preoperative treatment. Notably, MIE performed with no preoperative treatment was associated with significantly less incidence of any pulmonary morbidities, prolonged ventilation ≥48 hours, unplanned intubation, surgical site infection, and sepsis. However, reoperation within 30 days in patients with no preoperative treatment was frequently observed after MIE. The total surgery-related mortality rates of MIE and OE were 1.7% and 2.4%, respectively (P < 0.001). Increasing age, low preoperative activities of daily living, American Society of Anesthesiologists physical status ≥3, diabetes mellitus requiring insulin use, chronic obstructive pulmonary disease, congestive heart failure, creatinine ≥1.2 mg/dL, and lower hospital case volume were identified as independent risk factors for surgery-related mortality.

Conclusions:
The results suggest that MIE can replace OE in various situations from the perspective of short-term outcome.
Survey of Postoperative Activity Guidelines After Minimally Invasive Gynecologic and Pelvic Reconstructive Surgery
Authors: Winkelman William D. , Erlinger Adrienne L. , Haviland Miriam J. , Hacker Michele R. , Rosenblatt Peter L. 
Published: February 2019

Objective(s)
Most surgeons recommend restriction of activities after minimally invasive gynecologic and pelvic reconstructive surgery. The goal of this study was to identify and assess the postoperative guidelines gynecologists and urogynecologists provide their patients.

Methods
This was a cross-sectional study of physicians at a national gynecology conference in March 2018. Respondents were asked to answer questions about the typical postoperative recommendations they provide patients after gynecologic surgery as well as their postoperative prescribing habits.

Results
There were 418 attendees, and 135 (32%) eligible physicians completed the survey. Of respondents, 87% were specialists in female pelvic medicine and reconstructive surgery. Most respondents (61%) were in academic practice. Most respondents (82%–86%) recommended specific postoperative lifting restrictions, and 49% to 52% recommended limiting lifting to a maximum of 10 lb after surgery with some variation depending on the surgical procedure performed. Many respondents (42%–56% depending on the surgical procedure) recommended that patients wait at least 2 weeks before returning to sedentary work. Male respondents and those who were in practice for more than 10 years recommended that patients return to work sooner compared with those who were in practice less than 10 years. Male respondents prescribed fewer opioids to patients after vaginal hysterectomy (P = 0.04) and vaginal prolapse repair (P = 0.03) compared with female respondents.

Conclusions
After minimally invasive gynecologic or pelvic reconstructive surgery, providers recommend a wide range of postoperative restrictions and prescribe significantly different quantities of opioids during the postoperative period. This study highlights some of the recommendations with the greatest variability.
An Algorithm to Characterize a Dementia Population by Disease Subtype
Authors: Albrecht Jennifer S. , Hanna Maya , Randall Rhonda L. , Kim Dure , Perfetto Eleanor M. 
Published: February 2019

Purpose:
Identification of Alzheimer disease and related dementias (ADRD) subtypes is important for pharmacologic treatment and care planning, yet inaccuracies in dementia diagnoses make ADRD subtypes hard to identify and characterize. The objectives of this study were to (1) develop a method to categorize ADRD cases by subtype and (2) characterize and compare the ADRD subtype populations by demographic and other characteristics.

Methods:
We identified cases of ADRD occurring during 2008 to 2014 from the OptumLabs Database using diagnosis codes and antidementia medication fills. We developed a categorization algorithm that made use of temporal sequencing of diagnoses and provider type.

Results:
We identified 36,838 individuals with ADRD. After application of our algorithm, the largest proportion of cases were nonspecific dementia (41.2%), followed by individuals with antidementia medication but no ADRD diagnosis (15.6%). Individuals with Alzheimer disease formed 10.2% of cases. Individuals with vascular dementia had the greatest burden of comorbid disease. Initial documentation of dementia occurred primarily in the office setting (35.1%).

Discussion:
Our algorithm identified 6 dementia subtypes and three additional categories representing unique diagnostic patterns in the data. Differences and similarities between groups provided support for the approach and offered unique insight into ADRD subtype characteristics.
A semi-automatic dispenser for solid and liquid food in aquatic facilities
Authors: Candelier Raphaël , Bois Alex , Tronche Stéphane , Mahieu Jéremy , Mannioui Abdelkrim 
Published: February 2019

AbstractWe present a novel, low-footprint and low-cost semi-automatic system for delivering solid and liquid food to zebrafish, and more generally to aquatic animals raised in racks of tanks. It is composed of a portable main module equipped with a contactless reader that adjusts the quantity to deliver for each tank, and either a solid food module or a liquid food module. Solid food comprises virtually any kind of dry powder or grains below two millimeters in diameter, and, for liquid-mediated food, brine shrimps (Artemia salina) and rotifers (Rotifera) have been successfully tested. Real-world testing, feedback and validation have been performed in a zebrafish facility for several months. In comparison with manual feeding this system mitigates the appearance of musculoskeletal disorders among regularly-feeding staff, and let operators observe the animals’ behavior instead of being focused on quantities to deliver. We also tested the accuracy of both humans and our dispenser and found that the semi-automatic system is much more reliable, with respectively 7-fold and 84-fold drops in standard deviation for solid and liquid food.
Integrating transcriptomic network reconstruction and QTL analyses reveals mechanistic connections between genomic architecture andBrassica rapadevelopment
Authors: Baker Robert L. , Leong Wen Fung , T. Brock Marcus , Rubin Matthew J. , Markelz R. J. Cody , Welch Stephen , N. Maloof Julin , Weinig Cynthia 
Published: February 2019

ABSTRACTPlant developmental dynamics can be heritable, genetically correlated with fitness and yield, and undergo selection. Therefore, characterizing the mechanistic connections between the genetic architecture governing plant development and the resulting ontogenetic dynamics of plants in field settings is critically important for agricultural production and evolutionary ecology. We use a hierarchical Bayesian Function-Valued Trait (FVT) approach to estimateBrassica rapagrowth curves throughout ontogeny, across two treatments and in two growing seasons. We find that the shape of growth curves is relatively plastic across environments compared to final height, and that there are trade-offs between growth rate and duration. We determined that combining FVT Quantitative Trait Loci (QTL) and genes/eigengene expression identified via transcriptomic co-expression network reconstructions best characterized phenotypic variation. Further, targeted eQTL analyses identified regulatory hotspots that colocalized with FVT QTL and co-expression network identified genes and mechanistically link FVT QTL with structural trait variation throughout development in agroecologically relevant field settings.
Lactate and pyruvate promote cellular stress resistance and longevity through ROS signaling
Authors: Tauffenberger Arnaud , Fiumelli Hubert , Almustafa Salam , Magistretti Pierre J. 
Published: February 2019

SummaryL-lactate, for long considered a glycolytic end-product, is now recognized as an important energy substrate. Moreover, it appears that its role is not limited to energy production but also as a signal for neuroprotection and synaptic plasticity. Using a model of neuroblastoma cells and the nematode C. elegans we investigated the cellular mechanisms underlying this protective role of L-lactate. We found that L-lactate promotes a mild Reactive Oxygen Species (ROS) induction that translates into activation of antioxidant defenses and pro-survival pathways such as PI3K/AKT and Endoplasmic Reticulum (ER) chaperones. This hormetic mechanism provides protection against oxidative stress in both cells and nematodes. Furthermore, a mild ROS induction by lactate also promotes longevity in C. elegans.
Protein appetite drives macronutrient-related differences in ventral tegmental area neural activity
Authors: Chiacchierini Giulia , Naneix Fabien , Peters Kate Zara , Apergis-Schoute John , Simone Snoeren Eelke Mirthe , McCutcheon James Edgar 
Published: February 2019

AbstractControl of protein intake is essential for numerous biological processes as several amino acids cannot be synthesized de novo, however, its neurobiological substrates are still poorly understood. In the present study, we combined in vivo fiber photometry with nutrient-conditioned flavor in a rat model of protein appetite to record neuronal activity in the ventral tegmental area (VTA), a central brain region for the control of food-related processes. In adult male rats, protein restriction increased preference for casein (protein) over maltodextrin (carbohydrate). Moreover, protein consumption was associated with a greater VTA response relative to carbohydrate. After initial nutrient preference, a switch from a normal balanced diet to protein restriction induced rapid development of protein preference but required extensive exposure to macronutrient solutions to induce greater VTA responses to casein. Furthermore, prior protein restriction induced long-lasting food preference and VTA responses. This study reveals that VTA circuits are involved in protein appetite in times of need, a crucial process for all animals to acquire an adequate amount of protein in their diet.Significance StatementAcquiring insufficient protein in one’s diet has severe consequences for health and ultimately will lead to death. In addition, a low level of dietary protein has been proposed as a driver of obesity as it can leverage up intake of fat and carbohydrate. However, much remains unknown about the role of the brain in ensuring adequate intake of protein. Here, we show that in a state of protein restriction a key node in brain reward circuitry, the ventral tegmental area, is activated more strongly during consumption of protein than carbohydrate. Moreover, although rats’ behavior changed to reflect new protein status, patterns of neural activity were more persistent and only loosely linked to protein status.
A fronto-temporo-parietal network disambiguates potential objects of joint attention
Authors: Kraemer P. M. , Görner M. , Ramezanpour H. , Dicke P. W. , Thier P. 
Published: February 2019

AbstractWe use the other’s gaze direction to identify her/his object of interest and to shift our attention to the same object, i.e. to establish joint attention. However, gaze direction may not be sufficient to unambiguously identify the object of interest as the other’s gaze may hit more than one object. In this case, the observer must use a priori information to disambiguate the object choice. Using fMRI, we suggest that the disambiguation is based on a 3-component network. A first component, the well-known ‘gaze following patch’ in the posterior STS is activated by gaze following per se. BOLD activity here is determined exclusively by the usage of gaze direction and is independent of the need to disambiguate the relevant object. On the other hand, BOLD activity revealing a priori information for the disambiguation and starting early enough to this end is confined to a patch of cortex at the inferior frontal junction. Finally, BOLD activity reflecting the convergence of both, a priori information and gaze direction, needed to shift attention to a particular object location is confined to the posterior parietal cortex.
Proteomic and Transcriptomic Profiling Identifies Mediators of Anchorage-Independent Growth and Roles of Inhibitor of Differentiation Proteins in Invasive Lobular Breast Cancer
Authors: Tasdemir Nilgun , Ding Kai , Levine Kevin M. , Du Tian , Bossart Emily A. , Lee Adrian V. , Davidson Nancy E. , Oesterreich Steffi 
Published: February 2019

AbstractBACKGROUNDInvasive lobular carcinoma (ILC) is a histological subtype of breast cancer with distinct molecular and clinical features from the more common subtype invasive lobular carcinoma (IDC). We have previously shown that human ILC cells lines have a remarkably unique ability to grow in ultra-low attachment (ULA) suspension cultures as compared to IDC cells, the mediators of which remain unknown.METHODSUsing flow cytometry and immunoblotting in human ILC and IDC cell lines, we measured levels of apoptosis and cell proliferation in attached (2D) and suspension (ULA) cultures. siRNA-mediated knockdown and pharmacological inhibitors were utilized to assess the effects of known regulators of anchorage-independence. Reverse Phase Protein Arrays and RNA-Sequencing were performed to identify novel proteomic and transcriptomic mediators of ULA growth in ILC cells.RESULTSWe show that human ILC cell lines exhibit enhanced anoikis resistance and cell proliferation in ULA cultures as compared to IDC cells. Transient restoration of E-cadherin did not impact the 2D or ULA growth of human ILC cell lines, while transient E-cadherin knockdown in IDC cells partially rescued their growth defect in ULA culture. Inhibition of the Rho/ROCK, p120-catenin or YAP/Hippo pathways previously implicated in anoikis resistance did not have a major effect on the ULA growth of ILC cells. Proteomic comparison of ILC and IDC cell lines identified unique induction of PI3K/Akt and p90-RSK pathways in ULA culture in ILC cells. Transcriptional profiling uncovered unique upregulation of the Inhibitors of Differentiation family transcription factors ID1 and ID3 in ILC ULA culture, the knockdown of which diminished anchorage-independent growth. We find that ID1 and ID3 expression is higher in human ILC tumors as compared to IDC and correlated with a worse disease-specific survival uniquely in the ILC cohort.CONCLUSIONOur comprehensive study of 2D and ULA growth in human ILC cell lines revealed anoikis resistance, cell proliferation and novel mediators of anchorage-independence and provides possible mechanistic insights and clinical implications for metastatic dissemination of ILC. High expression in human ILC tumors and association with clinical outcome implicate ID1 and ID3 as novel drivers and therapeutic targets for lobular breast cancer.
Endogenous oxytocin inhibits hypothalamic stress responsive neurons following acute hypernatremia
Authors: Pati Dipanwita , Harden Scott W. , Kelly Kyle B. , de Kloet Annette D. , Krause Eric G. , Frazier Charles J. 
Published: February 2019

AbstractSignificant prior evidence indicates that centrally acting oxytocin robustly modulates stress responsiveness and anxiety-like behavior, although the neural mechanisms behind these effects are not completely understood. A plausible neural basis for oxytocin mediated stress reduction is via inhibition of corticotropin-releasing hormone (CRH) neurons in the paraventricular nucleus of the hypothalamus (PVN) that regulate activation of the hypothalamic-pituitary-adrenal (HPA) axis. Previously, we have shown that following subcutaneous injection of 2.0 M NaCl, oxytocin (OT) synthesizing neurons are activated in the rat PVN, an oxytocin receptor (Oxtr) dependent inhibitory tone develops on a subset of parvocellular neurons, and stress-mediated increases in plasma corticosterone levels are blunted. Here, we utilized transgenic male CRH-reporter mice to selectively target PVN CRH neurons for whole-cell recordings. These experiments reveal that acute salt loading produces tonic inhibition of PVN CRH neurons through a mechanism that is largely independent of synaptic activity. Further studies reveal that CRH neurons within the PVN synthesize mRNA for Oxtr(s). Salt induced Oxtr-dependent inhibitory tone was eliminated in individual PVN CRH neurons filled with GDP-β-S, and was also largely absent in PVN CRH neurons extracted form CRH-Oxtr KO mice. Additional electrophysiological studies suggest that reduced excitability of PVN CRH neurons in salt loaded animals is associated with increased activation of an inwardly rectifying potassium channel. Collectively, these data reveal a likely cellular mechanism by which endogenous oxytocin signaling reduces the excitability of PVN CRH neurons to curb stress responsiveness during times of high plasma osmolality.
The molecular basis of hypercontractility caused by the hypertrophic cardiomyopathy mutations R403Q and R663H
Authors: Sarkar Saswata S. , Trivedi Darshan V. , Morck Makenna M. , Adhikari Arjun S. , Pasha Shaik N. , Ruppel Kathleen M. , Spudich James A. 
Published: February 2019

AbstractHypertrophic cardiomyopathy (HCM) mutations in ß-cardiac myosin and myosin binding protein-C (MyBP-C) cause hypercontractility of the heart. We show that hypercontractility caused by the HCM myosin mutation R663H cannot be explained by changes in the fundamental parameters such as actin-activated ATPase, intrinsic force, velocity of pure actin or regulated thin filaments, or the pCa50 of the velocity of regulated thin filaments. The same conclusion was made earlier for the HCM myosin mutation R403Q (Nag et al. 2015). Using enzymatic assays for the number of functionally-available heads in purified human ß-cardiac myosin preparations, we provide evidence that both R403Q and R663H HCM myosin mutations cause hypercontractility by increasing the number of functionally-accessible myosin heads. We also demonstrate that the myosin mutation R403Q, but not R663H, ablates the binding of myosin with the C0-C7 fragment of myosin binding protein-C.
Performance of neural network basecalling tools for Oxford Nanopore sequencing
Authors: Wick Ryan R. , Judd Louise M. , Holt Kathryn E. 
Published: February 2019

AbstractBasecalling, the computational process of translating raw electrical signal to nucleotide sequence, is of critical importance to the sequencing platforms produced by Oxford Nanopore Technologies (ONT). Here we examine the performance of different basecalling tools, looking at accuracy at the level of bases within individual reads and at majority-rules consensus basecalls in an assembly. We also investigate some additional aspects of basecalling: training using a taxon-specific dataset, using a larger neural network model and improving consensus basecalls in an assembly via additional signal-level analysis with Nanopolish. Training basecallers on taxon-specific data resulted in a significant boost in consensus accuracy, mostly due to the reduction of errors in methylation motifs. A larger neural network was able to improve both read and consensus accuracy, but at a cost to speed. Improving consensus sequences (‘polishing’) with Nanopolish somewhat negates the accuracy differences in basecallers, but pre-polish accuracy does have an effect on post-polish accuracy, so basecaller choice is still relevant even when Nanopolish is used.
In-vitro pathogen inhibition: Comparing the inhibitory effects of a complex multistrain synbiotic with simple probiotics containing the yeast Saccharomyces boulardii or Lactobacillus rhamnosus bacteria
Authors: Piatek Jacek , Sommermeyer Henning , Ciechelska-Rybarczyk Arleta , Bernatek Malgorzata 
Published: February 2019

AbstractSupplementation with probiotics is considered as alternative treatment or adjuvant therapy for a number of bacterial infections for which the use of antibiotics is either not recommended or emerging antibiotic resistance is a major concern. Inhibition of the growth of pathogenic bacteria has been related to a number of different activities of probiotic bacteria or yeasts, some of which are very specific for particular strains of probiotics. As the different inhibition activities might act additively or even synergistically, probiotic multistrain products are discussed as potentially being more effective in pathogen inhibition than products containing one or a small number of probiotic strains. The present study investigated the in vitro inhibition of Escherichia (E.) coli, Shigella spp., Salmonella (S.) typhimurium and Clostridum (Cl.) difficile, all being human pathogens of significant worldwide healthcare concerns. The probiotic containing the yeast Sacharomyces (S.) boulardii inhibited all four pathogens. Similar inhibitions were observed with a bacterial probiotic containing three different strains (Pen, E/N and Oxy) of Lactobacillus (Lc.) rhamnosus. Compared to the inhibition found for these probiotics, the inhibitory effects of a complex multistrain synbiotic, containing nine different probiotic strains (6 Lactobacilli and 3 Bifidobacteria) and the prebiotic fructooligosaccharide (FOS), were significantly stronger. The stronger inhibition by the complex multistrain synbiotic was observed for all four tested pathogens. Our findings support a hypothesis that complex synbiotic products containing a larger number of different strains combined with a prebiotic component might be more attractive candidates for further clinical characterization than simpler probiotics containing one or only few probiotic strains.