bluuebunny/crossref_metadata_2025_split huggingface dataset:
HLA-haploidentische Stammzelltransplantation: Posttransplantations-Cyclophosphamid
Authors: Fraccaroli Alessia , Tischer Johanna 
Published: December 2017

ZusammenfassungIn der allogenen Blutstammzelltransplantation bezeichnet „haploidentisch“ einen Spender aus der Familie, der genetisch in den HLA-Merkmalen nur zu 50% mit seinem Empfänger übereinstimmt. Diese „Disparität“ stellt eine große immunologische Barriere für die Transplantation dar, die schwere Komplikationen wie Transplantatabstoßung, GvHD und Infektionen zur Folge haben kann. Dieses im Vergleich zur HLA-gematchten Transplantation erhöhte Risiko sowie aufwendige Herstellungsverfahren (In-vitro-Manipulation des Blutstammzellpräparats zur T-Zell-Depletion) zur Reduktion der aggressiven Immunogenität des Transplantats limitierten die Anwendung der HLA-haploidentischen Stammzelltransplantation bisher. Die unmanipulierte Haplo-HSZT mit Einsatz von Posttransplantations-Cyclophosphamid zur GvHD-Prophylaxe stellt ein neueres, simples und sicheres haploidentisches Transplantationsverfahren mit geringer Abstoßungsrate, guter hämatopoetischer Rekonstitution, wenig GvHD sowie günstiger Immunrekonstitution und wenig Infektionen dar. Somit ist bei niedriger TRM eine sichere Überwindung der HLA-Barriere mit guter Kontrolle der bidirektionalen Alloreaktivität möglich. Behandlungsergebnisse ähnlich wie bei einer HLA-kompatiblen Transplantation können erreicht werden. Andere alternative Transplantationsverfahren, wie die der MMUD-T, manipulierten Haplo-HSZT und CBT, treten aufgrund schlechterer Spenderverfügbarkeit und Verträglichkeit sowie aufwendiger Herstellungsverfahren in den Hintergrund. Die Verwendung eines sequenziellen Therapiekonzepts, das eine intensive Chemotherapie vor Start der Konditionierung zur Haplo-HSZT zur Reduktion der Leukämielast vorsieht, führt auch in der unmanipulierten Haplo-HSZT mit PTCY zu einer verbesserten Erkrankungskontrolle bei Patienten mit rezidivierter und refraktärer hämatologischer Erkrankung ohne Erhöhung der TRM..
Die durchflusszytometrische Verträglichkeitsprobe – sensitivere Diagnostik zur Prädiktion von Transplantatabstoßungen
Authors: Lindemann Monika , Heinold Andreas , Lenz Veronika , Horn Peter , Heinemann Falko 
Published: December 2017

ZusammenfassungBei der Lebendnierenspende hat man die Chance, das immunologische Risiko vor Transplantation sehr detailliert zu testen. Neben der Bestimmung der humanen Leukozytenantigene (HLA) ist die Suche nach HLA-Antikörpern und die Verträglichkeitsprobe (Crossmatch) zwingend erforderlich, wobei in Deutschland derzeit als Standard die komplementvermittelte Zytotoxizität gemessen wird (CDC-Crossmatch). Es geht darum, herauszufinden, ob der Empfänger präformierte spenderspezifische Antikörper hat, die eine Transplantatabstoßung auslösen können. Im Ausland, beispielsweise in Großbritannien, ist dagegen das durchflusszytometrische Crossmatch inzwischen als Standardverfahren etabliert. Dieses wurde bereits 1983 beschrieben und ist sensitiver als das CDC-Crossmatch. Es gibt inzwischen umfangreiche Studien, die zeigen, dass ein positives durchflusszytometrisches Crossmatch ein erhöhtes Risiko für antikörpervermittelte Abstoßungen anzeigt. Dies konnte in unserer Kohorte bestätigt werden, in der ein positives durchflusszytometrisches Crossmatch für die T-Zellen ein 10,1-fach und für die B-Zellen ein 3,2-fach erhöhtes Risiko anzeigt.
Laryngektomie: Prognosefaktoren für Liegedauer, Reoperation und Readmission
Authors: Jadeed Rawad 
Published: December 2017

Helman SN et al. Predictors of Stay, Reoperation, and Readmission Following Total Laryngektomie. Laryngoscope 2017; 127: 1339–1344
Nach totaler Laryngektomie kommt es in bis zu 34 % der Fälle zu Komplikationen. Die Rehospitalisierungsrate ist hoch und beträgt mehr als
26 %. Verlängerte stationäre Aufenthaltsdauer, ungeplante Rückkehr in der Operationssaal und stationäre Wiederaufnahme sind 3 Faktoren, die
hohe Kosten verursachen und wichtige Indikatoren der Versorgungsqualität darstellen. US-Forscher suchten diesbezüglich nach unabhängigen
perioperativen Risikofaktoren.
Protein kinase C and calcineurin cooperatively mediate cell survival under compressive mechanical stress
Authors: Mishra Ranjan , van Drogen Frank , Dechant Reinhard , Oh Soojung , Jeon Noo Li , Lee Sung Sik , Peter Matthias 
Published: December 2017

Significance
Cells are constantly exposed to a variety of mechanical cues, and respond by activating conserved signaling pathways that modulate their profiliation and intracellular organization. For instance, cells in solid tumors experience sustained compression from the microenvironment, and compressive stress is known to trigger an invasive phenotype in some cancer cells. However, despite its importance for health and disease, the specific mechanosensors and the downstream signaling network mediating these physiological responses remain largely unknown, in part due to the lack of appropriate experimental systems. Here, we develop a microfluidic platform that allows triggering compressive mechanical stress in a reversible and controllable manner, and we identify cell surface receptors that specifically sense compressive mechanical stress and generate synergistic cellular responses.
Carbon Monoxide Off-Gassing From Bags of Wood Pellets
Authors: Rahman Mohammad Arifur , Rossner Alan , Hopke Philip K 
Published: December 2017

Abstract
Wood pellets are increasingly used for space heating in the United States and globally. Prior work has shown that stored bulk wood pellets produce sufficient carbon monoxide (CO) to represent a health concern and exceed regulatory standards for occupational exposures. However, most of the pellets used for residential heating are sold in 40-pound (18.1 kg) plastic bags. This study measured CO emission factors from fresh, bagged-wood pellets as a function of temperature and relative humidity. CO concentrations increased with increasing temperature and moisture in the container. CO measurements in a pellet mill warehouse with stored pallets of bagged pellets had 8-h average CO concentrations up to 100 ppm exceeding occupational standards for worker exposure. Thus, manufacturers, distributors, and home owners should be aware of the potential for CO in storage areas and design facilities with appropriate ventilation and CO sensors.
Model-based design of bistable cell factories for metabolic engineering
Authors: Srinivasan Shyam , Cluett William R , Mahadevan Radhakrishnan 
Published: December 2017

Abstract

Motivation
Metabolism can exhibit dynamic phenomena like bistability due to the presence of regulatory motifs like the positive feedback loop. As cell factories, microorganisms with bistable metabolism can have a high and a low product flux at the two stable steady states, respectively. The exclusion of metabolic regulation and network dynamics limits the ability of pseudo-steady state stoichiometric models to detect the presence of bistability, and reliably assess the outcomes of design perturbations to metabolic networks.

Results
Using kinetic models of metabolism, we assess the change in the bistable characteristics of the network, and suggest designs based on perturbations to the positive feedback loop to enable the network to produce at its theoretical maximum rate. We show that the most optimal production design in parameter space, for a small bistable metabolic network, may exist at the boundary of the bistable region separating it from the monostable region of low product fluxes. The results of our analysis can be broadly applied to other bistable metabolic networks with similar positive feedback network topologies. This can complement existing model-based design strategies by providing a smaller number of feasible designs that need to be tested in vivo.

Availability and implementation
http://lmse.biozone.utoronto.ca/downloads/

Supplementary information
Supplementary data are available at Bioinformatics online.
Patient portal use and hospital outcomes
Authors: Dumitrascu Adrian G , Burton M Caroline , Dawson Nancy L , Thomas Colleen S , Nordan Lisa M , Greig Hope E , Aljabri Duaa I , Naessens James M 
Published: December 2017

Abstract

Objectives
To determine whether use of a patient portal during hospitalization is associated with improvement in hospital outcomes, 30-day readmissions, inpatient mortality, and 30-day mortality.

Materials and Methods
We performed a retrospective propensity score–matched study that included all adult patients admitted to Mayo Clinic Hospital in Jacksonville, Florida, from August 1, 2012, to July 31, 2014, who had signed up for a patient portal account prior to hospitalization (N = 7538).

Results
Out of the admitted patients with a portal account, 1566 (20.8%) accessed the portal while in the hospital. Compared to patients who did not access the portal, patients who accessed the portal were younger (58.8 years vs 62.3 years), had fewer elective admissions (54.2% vs 64.1%), were more frequently admitted to medical services (45.8% vs 35.2%), and were more likely to have liver disease (21.9% vs 12.9%) and higher disease severity scores (0.653 vs 0.456). After propensity score matching, there was no statistically significant difference between the 2 cohorts with respect to 30-day readmission (P = .13), inpatient mortality (P = .82), or 30-day mortality (P = .082).

Conclusion
Use of the patient portal in the inpatient setting may not improve hospital outcomes. Future research should examine the association of portal use with more immediate inpatient health outcomes such as patient experience, patient engagement, medication reconciliation, and prevention of adverse events.
Thoracic Epidural Analgesia and Mortality in Acute Pancreatitis: A Multicenter Propensity Analysis
Authors: Jabaudon Matthieu , Belhadj-Tahar Nouria , Rimmelé Thomas , Joannes-Boyau Olivier , Bulyez Stéphanie , Lefrant Jean-Yves , Malledant Yannick , Leone Marc , Abback Paer-Selim , Tamion Fabienne , Dupont Hervé , Lortat-Jacob Brice , Guerci Philippe , Kerforne Thomas , Cinotti Raphael , Jacob Laurent , Verdier Philippe , Dugernier Thierry , Pereira Bruno , Constantin Jean-Michel 
Published: December 2017

Objective:
Recent preclinical and clinical data suggest that thoracic epidural analgesia, a technique primarily aimed at decreasing pain, might exert anti-inflammatory effects, enhance splanchnic and pancreatic blood flow during acute pancreatitis; however, the influence of epidural analgesia on mortality remains under investigated in this setting. This study was therefore designed to assess the impact of epidural analgesia on mortality in ICU patients with acute pancreatitis.

Design:
Multicenter retrospective, observational, cohort study.

Setting:
Seventeen French and Belgian ICUs.

Patients:
All patients admitted to with acute pancreatitis between June 2009 and March 2014.

Interventions:
The primary exposure was thoracic epidural analgesia versus standard care without epidural analgesia. The primary outcome was 30-day mortality. Propensity analyses were used to control for bias in treatment assignment and prognostic imbalances.

Measurements and Main Results:
One thousand three ICU patients with acute pancreatitis were enrolled, of whom 212 died within 30 days. Epidural analgesia was used in 46 patients and was associated with reduced mortality in unadjusted analyses (4% vs. 22%; p = 0.003). After adjustment for baseline variables associated with mortality, epidural analgesia was still an independent predictor of 30-day mortality (adjusted odds ratio, 0.10; [95% CI, 0.02–0.49]; p = 0.004). Using propensity score analysis, the risk of all-cause 30-day mortality in patients with acute pancreatitis receiving epidural analgesia was significantly lower than that in matched patients who did not receive epidural analgesia (2% vs. 17%; p = 0.01).

Conclusions:
Among critically ill patients with acute pancreatitis, mortality at 30 days was lower in patients who received epidural analgesia than in comparable patients who did not. These findings support ongoing research on the use of epidural analgesia as a therapeutic intervention in acute pancreatitis.
Cosmetic Adolescent Filler: An Innovative Treatment of the “Selfie” Complex
Authors: Berros Philipe , Armstrong Blair K. , Foti Pauline , Mancini Ronald 
Published: December 2017

Purpose:
“Selfie” photography is increasing among teenagers, accentuates congenital anomalies, and impacts self-confidence. Tear trough deformity is most commonly due to aging, but also occurs as a congenital anomaly and can be a major source of insecurity and embarrassment.

Objective:
The purpose of this study is to show the efficacy and safety of hyaluronic acid gel filler in a teenage patient with congenital tear trough deformity.

Material and Method:
We describe the case of a teenager who underwent hyaluronic acid gel filling to the tear trough deformity at age 14 years. Prospective follow up was assessed for 5 years.

Results:
The patient improved clinical appearance and self confidence. Her satisfaction level was high, and no complication occurred during entire follow up.

Conclusion:
In this case, hyaluronic gel acid filler was safe and effective for augmentation of congenital tear trough. The patient was satisfied and experienced increased self-esteem.
Procedural pain and oral glucose in preterm neonates: brain development and sex-specific effects
Authors: Schneider Juliane , Duerden Emma G. , Guo Ting , Ng Karin , Hagmann Patric , Bickle Graz Myriam , Grunau Ruth E. , Chakravarty M. Mallar , Hüppi Petra S. , Truttmann Anita C. , Miller Steven P. 
Published: December 2017

Abstract
Our objectives were to determine whether procedural pain and glucose exposure are associated with altered structural and functional brain development differently in preterm males and females, and neurodevelopment at 18-month corrected age. Fifty-one very preterm neonates (22 males; median [interquartile range] gestational age 27.6 [2.0] weeks) underwent 3 serial scans including T1-weighted and resting-state functional magnetic resonance imaging (MRI) at median postmenstrual weeks: 29.4, 31.9, and 41.1. Thalamus, basal ganglia, and total brain volumes were segmented. Functional resting-state MRI data were extracted from the independent-components maps. Pain was operationalized as the total number of neonatal intensive care unit–administered invasive procedures. Neurodevelopmental outcomes at 18-month corrected age were assessed with the Bayley Scales of Infant Development, second edition. Generalized estimating equations assessed the association of pain and glucose exposure with brain structural and functional development. More invasive procedures were independently associated with slower growth of thalamic (P < 0.001), basal ganglia (P = 0.028), and total brain volumes (P = 0.001), particularly in females. Similar relationships were observed between glucose exposure and brain volumes. Functional connectivity between thalamus and sensorimotor cortices was negatively associated with number of invasive procedures. Greater procedural pain and higher glucose exposure were related to poorer neurodevelopmental outcomes. These findings suggest that structural and functional brain development is vulnerable to procedural pain. Glucose used for analgesia does not appear to mitigate the adverse impact of pain on brain development. The vulnerability of brain development in females towards early pain is distinct from other neonatal morbidities. The link between pain and glucose with neurodevelopment suggests that these factors have long-lasting impact.
Self-Reported Mild Traumatic Brain Injuries in Relation to Rumination and Depressive Symptoms: Moderating Role of Sex Differences and a Brain-Derived Neurotrophic Factor Gene Polymorphism
Authors: Gabrys Robert L. , Dixon Kaylyn , Holahan Matthew R. , Anisman Hymie 
Published: December 2017

Objective:
Mild traumatic brain injuries (mTBIs) have frequently been associated with the emergence and persistence of depressive symptoms. However, the factors which contribute to the increased risk for depression after these head injuries remain unclear. Accordingly, we examined the relationship between frequency of self-reported mTBIs and current symptoms of depression and the mediating role of rumination and cognitive flexibility. We also examined whether these relations were moderated by sex differences and the presence of the Val66Met polymorphism in a gene coding for brain-derived neurotrophic factor (BDNF).

Design:
Retrospective, cross-sectional.

Setting:
Carleton University.

Participants:
Two hundred nineteen Carleton University undergraduate students.

Main Outcome Measures:
Cognitive flexibility as assessed by the Wisconsin Card Sorting Task (WCST); subtypes of rumination (Ruminative Response Scale; Treynor, Gonzalez, and Nolen-Hoeksema, 2003); depressive symptoms (Beck Depression Inventory; Beck, Ward, and Mendelson, 1961).

Results:
Greater frequency of self-reported mTBIs was associated with more frequent depressive rumination among women, but not men, which was accompanied by elevated current depressive symptoms. In addition, among Met allele carriers of the BDNF polymorphism, but not those who were Val homozygotes, greater frequency of mTBIs was related to higher levels of brooding, which was accompanied by heightened depressive symptoms. Brain-derived neurotrophic factor genotype also moderated the relationship between self-reported mTBIs and cognitive flexibility in that more frequent mTBIs were associated with more perseverative errors on the WCST among Met carriers, but not Val homozygotes.

Conclusions:
The present findings raise the possibility that the evolution of depression after mTBIs may be dependant on a BDNF polymorphism and sex differences.
Statistical methods for large ensemble of super-resolution stochastic single particle trajectories
Authors: Hoze N. , Holcman D. 
Published: December 2017

AbstractFollowing recent progresses in super-resolution microscopy obtained in the last decade, massive amount of redundant single stochastic trajectories are now available for statistical analysis. Flows of trajectories of molecules or proteins are sampling the cell membrane or its interior at a very high time and space resolution. Several statistical analysis were developed to extract information contained in these data, such as the biophysical parameters of the underlying stochastic motion to reveal the cellular organization. These trajectories can further reveal hidden subcellular organization. We present here the statistical analysis of these trajectories based on the classical Langevin equation, which serves as a model of trajectories. Parametric and non-parametric estimators are constructed by discretizing the stochastic equations and they allow recovering tethering forces, diffusion tensor or membrane organization from measured trajectories, that differ from physical ones by a localization noise. Modeling, data analysis and automatic detection algorithms serve extracting novel biophysical features such as potential wells and other sub-structures, such as rings at an unprecedented spatiotem-poral resolution. It is also possible to reconstruct the surface membrane of a biological cell from the statistics of projected random trajectories.
Peripatric speciation associated with genome expansion and female-biased sex ratios in the moss genus Ceratodon
Authors: Nieto-Lugilde Marta , Werner Olaf , McDaniel Stuart F. , Koutecký Petr , Kučera Jan , Rizk Samah Mohamed , Ros Rosa M. 
Published: December 2017

ABSTRACTPREMISE OF THE STUDYA period of allopatry is widely believed to be essential for the evolution of reproductive isolation. However, strict allopatry may be difficult to achieve in some cosmopolitan, spore-dispersed groups, like mosses. Here we examine the genetic and genome size diversity in Mediterranean populations of the moss Ceratodon purpureus s.l. to evaluate the role of allopatry and ploidy change in population divergence.METHODSWe sampled populations of the genus Ceratodon from mountainous areas and lowlands of the Mediterranean region, and from western and central Europe. We performed phylogenetic and coalescent analyses on sequences from five nuclear introns and a chloroplast locus to reconstruct their evolutionary history. We also estimated the genome size using flow cytometry, employing propidium iodide, and determined their sex using a sex-linked PCR marker.KEY RESULTSTwo well differentiated clades were resolved, discriminating two homogeneous groups: the widespread C. purpureus and a local group mostly restricted to the mountains in southern Spain. The latter also possessed a genome size 25% larger than the widespread C. purpureus, and the samples of this group consist entirely of females. We also found hybrids, and some of them had a genome size equivalent to the sum of the C. purpureus and Spanish genome, suggesting that they arose by allopolyploidy.CONCLUSIONSThese data suggest that a new species of Ceratodon arose via peripatric speciation, potentially involving a genome size change and a strong female-biased sex ratio. The new species has hybridized in the past with C. purpureus.
Classifying cells with Scasat - a tool to analyse single-cell ATAC-seq
Authors: Baker Syed Murtuza , Rogerson Connor , Hayes Andrew , Sharrocks Andrew D. , Rattray Magnus 
Published: December 2017

AbstractMotivationThe assay for transposase-accessible chromatin using sequencing (ATAC-seq) reveals the landscape and principles of DNA regulatory mechanisms by identifying the accessible genome of mammalian cells. When done at single-cell resolution, it provides an insight into the cell-to-cell variability that emerges from identical DNA sequences by identifying the variability in the genomic location of open chromatin sites in each of the cells. Processing of single-cell ATAC-seq requires a number of steps and a simple pipeline to processes and analyse single-cell ATAC-seq is not yet available.ResultsThis paper presents ScAsAT (single-cell ATAC-seq analysis tool), a complete pipeline to process scATAC-seq data with simple steps. The pipeline is developed in a Jupyter notebook environment that holds the executable code along with the necessary description and results. For the initial sequence processing steps, the pipeline uses a number of well-known tools which it executes from a python environment for each of the fastq files. While functions for the data analysis part are mostly written in R, it is robust, flexible, interactive and easy to extend. The pipeline was applied to a single-cell ATAC-seq dataset in order to identify different cell-types from a complex cell mixture. The results from Scasat showed that open chromatin location corresponding to potential regulatory elements can account for cellular heterogeneity and can identify regulatory regions that separates cells from a complex population.AvailabilityThe jupyter notebook with the complete pipeline applied to the dataset published with this paper are publicly available on the Github (https://github.com/ManchesterBioinference/Scasat). An additional notebook is also provided for analysis of a publicly available dataset. The fastq files are submitted at ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-6116.Contactsyed.murtuzabaker@manchester.ac.uk and magnus.rattray@manchester.ac.ukSupplementary informationSupplementary data are available at bioRxiv online.