bluuebunny/crossref_metadata_2025_split huggingface dataset:
A two-miRNA signature (miR-33a-5p and miR-128-3p) in whole blood as potential biomarker for early diagnosis of lung cancer
Authors: Pan Jinchang , Zhou Chengwei , Zhao Xiaodong , He Jinxian , Tian Hui , Shen Weiyu , Han Ying , Chen Jun , Fang Shuai , Meng Xiaodan , Jin Xiaofeng , Gong Zhaohui 
Published: November 2018

AbstractMicroRNAs (MiRNAs) have been found to be dysregulated in lung cancer tissues compared to their matched paracancerous tissues. However, the roles of miRNAs in peripheral blood as potential biomarkers for early diagnosis of lung cancer remain poorly understood. Here we found that miR-33a-5p and miR-128-3p were down-regulated in lung cancer tissues and cell lines. The expression levels of miR-33a-5p and miR-128-3p in lung cancer tissues were significantly correlated to TNM stages. MiR-128-3p in lung cancer tissues was also remarkably related to smoking and tumor size. The relative expression levels of miR-33a-5p and miR-128-3p were positively correlated in lung cancer tissues. Notably, miR-33a-5p and miR-128-3p in whole blood of lung cancer patients or early-stage lung cancer patients (TNM stage I-II) were lowly expressed as compared with that in healthy controls. The receiver operating characteristic curve (ROC) analyses revealed higher area under the ROC curve (AUC) values and higher sensitivity/specificity of miR-33a-5p and miR-128-3p alone and in combination were superior to that of traditional tumor markers (CYFR21-1, NSE and CA72-4). Importantly, both miR-33a-5p and miR-128-3p in whole blood were highly stable even under different harsh conditions. The results demonstrate that tumor suppressor miR-33a-5p/miR-128-3p in whole blood can serve as novel biomarkers for the early detection of lung cancer.
A global dataset of air temperature derived from satellite remote sensing and weather stations
Authors: Hooker Josh , Duveiller Gregory , Cescatti Alessandro 
Published: November 2018

AbstractAir temperature at 2 m above the land surface is a key variable used to assess climate change. However, observations of air temperature are typically only available from a limited number of weather stations distributed mainly in developed countries, which in turn may often report time series with missing values. As a consequence, the record of air temperature observations is patchy in both space and time. Satellites, on the other hand, measure land surface temperature continuously in both space and time. In order to combine the relative strengths of surface and satellite temperature records, we develop a dataset in which monthly air temperature is predicted from monthly land surface temperature for the years 2003 to 2016, using a statistical model that incorporates information on geographic and climatic similarity. We expect this dataset to be useful for various applications involving climate monitoring and land-climate interactions.
Akute Promyelozyten-Leukämie: Neue Behandlungsstrategien mit ATRA und ATO – AML-BFM-Empfehlungen
Authors: Creutzig Ursula , Dworzak Michael , von Neuhoff Nils , Rasche Mareike , Reinhardt Dirk 
Published: November 2018

ZusammenfassungDie Behandlung der Akuten Promyelozyten-Leukämie (APL) hat sich in den letzten Jahren deutlich geändert. Heute können APL Patienten mit Standardrisiko – (auch als Niedrigrisiko bezeichnet) ohne Chemotherapie nur mit all-trans-Retinsäure (ATRA) und Arsentrioxid (ATO) behandelt werden. Bei Hochrisikopatienten sollte eine Induktions-Chemotherapie hinzugefügt werden. Die kurativen Ergebnisse sind gut und vergleichbar mit jenen, die in der Vergangenheit mit Chemotherapie plus ATRA erzielt wurden. Toxizitäten, insbesondere infektiöse Komplikationen sind jedoch deutlich seltener. Das Hauptrisiko bleiben frühe letale Blutungen. Durch rechtzeitige Diagnose und frühe ATRA-Behandlung kann dieses Risiko reduziert werden. In der vorliegenden Übersicht werden die aktuellen Behandlungsstrategien und Empfehlungen für APL bei Kindern dargestellt und diskutiert.
Associations of Bone Mineral Density and Bone Metabolism Indices with Urine Albumin to Creatinine Ratio in Chinese Patients with Type 2 Diabetes
Authors: Zhao Xin , Zhang Xiao-Mei , Yuan Ning , Yu Xiao-Feng , Ji Li-Nong 
Published: November 2018

Abstract
Objective To identify correlations of bone mineral density (BMD) and bone metabolism indices with the urine albumin to creatinine ratio (ACR) as an indicator of nephropathy in Chinese patients with type 2 diabetes (T2D).
Methods In this retrospective analysis, 297 patients with T2D were divided into 3 groups according to the urine ACR. Patients’ data were analyzed to identify associations of general conditions, blood glucose level, lipid levels, and uric acid level with BMD and bone metabolism indices.
Results BMD at every location tested (femoral neck, trochanter, inside hip, Ward’s triangle, total hip, and lumbar vertebrae) was negatively correlated with the urine ACR (all p<0.05). Osteocalcin, beta-C-terminal telopeptide (β-CTX), and procollagen type 1 N- peptide (P1NP) were positively correlated with urine ACR (all p<0.05). Finally, 25-hydroxyvitamin D [25(OH)D] was negatively correlated with urine ACR (p<0.05). Multiple regression analysis with adjustment for age, body mass index, disease duration, and other clinical measurements revealed no significant correlation between urine ACR and BMD measurements or β-CTX (p>0.05). However, significant correlations remained between urine ACR and osteocalcin, P1NP, and 25(OH)D (p<0.05). The same results were obtained for postmenopausal women specifically, with the exception of a significant correlation between the ACR and β-CTX (p<0.05).
Conclusion In the early stage of diabetic nephropathy, BMD changes and bone transformation acceleration may occur, and the acceleration of bone transformation may occur before the change in BMD. Therefore, it is important to monitor bone metabolism indices in the early stage of diabetic nephropathy in T2D patients.
Efficacy of Caregivers’ Intervention on Recovery of Head Injury Cases in India
Authors: Verma Kirti , Tewari Manoj , Kaur Sukhpal , Ghai Sandhya ,   Shruti
Published: November 2018

Abstract
Background Patients with head injury are discharged from hospitals in a dependent state. In the home care settings, the caregivers have to take care of the patients. In India, there is scarcity of data on interventions of family caregivers of persons with head injuries.
Objective To assess the efficacy of an instructional module for caregivers of patients with head injury on recovery of the patients.
Method The study was performed at the Neuro-Surgery Department of Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India. Total 82 patients with 41 each in experimental and control groups and their caregivers were included in the study. The caregivers of patients in experimental group were demonstrated procedures related to care of a dependent patient. An instructional module containing guidelines regarding personal hygiene, catheter care at home, prevention of bedsores, tracheostomy suctioning at home, range-of-motion exercises, care of surgical wound, and discharge instructions regarding medication and follow-up was given to the caregivers in experimental group. The efficacy of intervention was assessed on occurrence of fever, chest infection, eye infection, bedsores, wound infection, constipation, urinary tract infection, deep vein thrombosis, length of stay, and readmission in hospital in both the groups.
Results Occurrence of fever, constipation, and length of stay were reduced significantly in experimental group. A reduction in the rates of chest infection, bedsore development, wound infection, and urinary tract infection were also noted in experimental group.
Conclusion The study shows that training the caregivers of head injury patients enhances the recovery and prevents complications in the patients.
Efficacy of Liposomal Bupivacaine Compared with Multimodal Periarticular Injections for Postoperative Pain Control following Total Knee Arthroplasty
Authors: Britten Tyler , Hughes Jonathan D. , Munoz Maldonado Yolanda , Hitt Kirby D. 
Published: November 2018

AbstractSingle-dose long-acting periarticular anesthetics have been shown to be an effective method of postoperative analgesia in total knee arthroplasty (TKA). This study retrospectively compares the efficacy of multimodal periarticular injection consisting of a combination of ropivacaine, duramorph, epinephrine, and toradol (HC) with liposomal bupivacaine (LB) periarticular injection in TKA. This study was a retrospective matched comparative chart review of two cohorts of patients who underwent TKA within a single health care system and cared for by one provider. We compared 22 patients who were treated with LB intraoperatively (LBG) with 41 matched controls who were treated with HC periarticular injection (HCG). These cases were retrospectively reviewed at 0 to 6, 6 to 12, 12 to 24, 24 to 48, and 48 to 72 hours. We reviewed pain scores and opioid use per the preceding time period, total opioid use, length of stay (LOS), and wound complications between the two groups. The two groups showed no statistical difference in total opioids used. In both the 6- to 12-hour and 12- to 24-hour intervals, the LBG required significantly more opioids than the HCG, with p-values of 0.0039 and 0.0061, respectively. Pain scores were not significantly different for any time period. We found no difference in LOS. The LBG tended to have lower doses of antiemetics than the HCG. No significant difference was found in postoperative pain scores and total opioid use between LB and multimodal periarticular intraoperative injections in TKA. Our data demonstrated decreased opioid consumption in the HC group compared with the LB group in both the 6- to 12-hour and 12- to 24-hour time intervals postoperatively. At our institution, LB costs US$314.99, whereas HC costs US$95.
Histological Findings in Infected and Noninfected Second Stage Revision Knee Arthroplasties
Authors: Uchihara Yoshinobu , Inagaki Yusuke , Munemoto Mitsuru , Tanaka Yasuhito , Athanasou Nicholas 
Published: November 2018

AbstractTissues from a periprosthetic joint infection (PJI) of the knee contain a heavy neutrophil polymorph (NP) infiltrate (> 5 NPs per high-powered field [HPF] by Musculoskeletal Infection Society [MSIS] criteria). PJI of the knee can be treated by a two-stage procedure and our aim was to determine whether the MSIS histological criteria for PJI diagnosis are valid in a second-stage revision knee arthroplasty. Periprosthetic tissues from 45 second-stage revision knee cases were analyzed histologically by hematoxylin–eosin and chloroacetate esterase (CAE) staining for the identification of NPs. The number of NPs was determined semiquantitatively and results correlated with the microbiological and clinical findings. In 9 of the 45 cases, an organism was cultured in two or more samples, meeting MSIS microbiological criteria for a definite diagnosis of PJI; histologically, seven of these cases contained > 5 per NPs per HPF on average, with the remaining two cases containing 1 NP and 2 NPs per HPF. In noninfected second-stage revisions, NPs were not seen in 30 cases with 6 cases showing less than 1 NP per HPF on average. The sensitivity, specificity, accuracy, and positive and negative predictive values of MSIS histological criteria (> 5 NPs per HPF) to diagnose PJI were 78%, 100%, 96%, 100%, and 95%, respectively. MSIS histological criteria for the diagnosis of PJI are valid for most but not all infected second-stage revision knee arthroplasties. Correlation of histology with clinical, microbiology and other laboratory findings is required to establish a diagnosis of PJI in second-stage revision knee arthroplasties.
Case Series about the Changed Antiplatelet Protocol for Carotid Endarterectomy in a Teaching Hospital: More Patients with Complications?
Authors: Marsman Martijn , Özdemir- van Brunschot Denise , Jahrome Abdelkarime , Veeger Nic , Schuiling Wouter , van Rooij Frank , Koning Giel 
Published: November 2018

Introduction In the Netherlands, clopidogrel monotherapy increasingly replaces acetylsalicylic acid and extended release dipyridamole as the first-choice antiplatelet therapy after ischemic stroke. It is unknown whether the risk of peri- and postoperative hemorrhage in carotid artery surgery is higher in patients using clopidogrel monotherapy compared with acetylsalicylic acid and extended release dipyridamole. We therefore retrospectively compared occurrence of perioperative major and (clinical relevant) minor bleedings during and after carotid endarterectomy of two groups using different types of platelet aggregation inhibition after changing our daily practice protocol in our center.
Material and Methods A consecutive series of the most recent 80 carotid endarterectomy patients (November 2015–August 2017) treated with the new regime (clopidogrel monotherapy) were compared with the last 80 (January 2012–November 2015) consecutive patients treated according to the old protocol (acetylsalicylic acid and dipyridamole). The primary endpoint was any major bleeding during surgery or in the first 24 to 72 hours postoperatively. Secondary outcomes within 30 days after surgery included minor (re)bleeding postoperative stroke with persistent or transient neurological deficit, persisting or transient neuropraxia, asymptomatic restenosis or occlusion, (transient) headache. Reporting of this study is in line with the ‘Strengthening the Reporting of Observational Studies in Epidemiology’ statement.
Results Although statistical differences were observed, from a clinical perspective both patients groups were comparable. Postoperative hemorrhage requiring reexploration for hemostasis occurred in none of the 80 patients in the group of the clopidogrel monotherapy (new protocol) and it occurred in one of the 80 patients (1%) who was using acetylsalicylic acid and dipyridamole (old protocol). In three patients (4%) in the clopidogrel monotherapy and one patient (1%) in the acetylsalicylic acid and extended release dipyridamole protocol an ipsilateral stroke was diagnosed.
Conclusion In this retrospective consecutive series the incidence of postoperative ischemic complications and perioperative hemorrhage after carotid endarterectomy (CEA) seemed to be comparable in patients using clopidogrel monotherapy versus acetylsalicylic acid and extended release dipyridamole for secondary prevention after a cerebrovascular event. This study fuels the hypothesis that short- and midterm complications of clopidogrel and the combination acetylsalicylic acid and extended release dipyridamole are comparable.
Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse
Authors: Yeom Kyu-Hyeon , Mitchell Simon , Linares Anthony J. , Zheng Sika , Lin Chia-Ho , Wang Xiao-Jun , Hoffmann Alexander , Black Douglas L. 
Published: November 2018

Significance
MicroRNAs repress genes controlling important decisions in animal development, but miRNA production and their interaction with larger genetic programs of development are not well understood. We found that the initial transcript of an important neuronal miRNA, miR-124, is expressed much earlier in development than the mature functional miRNA. Conversion of this primary RNA into its active form is blocked by the RNA binding protein PTBP1, whose down-regulation upon neuronal differentiation allows mature miR-124 expression. To understand the need for this regulation, we developed a mathematical model of the PTBP1/miR-124 regulatory circuit, finding that early expression of unprocessed miR-124 creates a sharp transition in gene expression during neuronal differentiation, making this developmental decision less affected by random variation and noise.
Acoustic phonon lifetimes limit thermal transport in methylammonium lead iodide
Authors: Gold-Parker Aryeh , Gehring Peter M. , Skelton Jonathan M. , Smith Ian C. , Parshall Dan , Frost Jarvist M. , Karunadasa Hemamala I. , Walsh Aron , Toney Michael F. 
Published: November 2018

Significance
Hybrid organic–inorganic perovskites are a promising class of materials for efficient and low-cost solar cells. Unlike conventional inorganic semiconductors such as silicon and gallium arsenide, hybrid perovskites feature significant dynamic disorder in their crystal structure. This dynamic disorder can be broadly classified into lattice vibrations (phonons) and molecular rotations. Phonons interact with charge carriers through electron–phonon coupling, which has substantial impacts on the operation of solar cells. Our study shows that acoustic phonons, the type responsible for transmitting heat in conventional semiconductors, have extraordinarily short lifetimes in the archetypal hybrid perovskite methylammonium lead iodide. These short lifetimes have direct implications on the cooling and transport of electrons and reflect a key difference between hybrid perovskites and conventional photovoltaic semiconductors.
dtangle: accurate and robust cell type deconvolution
Authors: Hunt Gregory J , Freytag Saskia , Bahlo Melanie , Gagnon-Bartsch Johann A 
Published: November 2018

Abstract

Motivation
Cell type composition of tissues is important in many biological processes. To help understand cell type composition using gene expression data, methods of estimating (deconvolving) cell type proportions have been developed. Such estimates are often used to adjust for confounding effects of cell type in differential expression analysis (DEA).

Results
We propose dtangle, a new cell type deconvolution method. dtangle works on a range of DNA microarray and bulk RNA-seq platforms. It estimates cell type proportions using publicly available, often cross-platform, reference data. We evaluate dtangle on 11 benchmark datasets showing that dtangle is competitive with published deconvolution methods, is robust to outliers and selection of tuning parameters, and is fast. As a case study, we investigate the human immune response to Lyme disease. dtangle’s estimates reveal a temporal trend consistent with previous findings and are important covariates for DEA across disease status.

Availability and implementation
dtangle is on CRAN (cran.r-project.org/package=dtangle) or github (dtangle.github.io).

Supplementary information
Supplementary data are available at Bioinformatics online.
Whisper: read sorting allows robust mapping of DNA sequencing data
Authors: Deorowicz Sebastian , Debudaj-Grabysz Agnieszka , Gudyś Adam , Grabowski Szymon 
Published: November 2018

Abstract

Motivation
Mapping reads to a reference genome is often the first step in a sequencing data analysis pipeline. The reduction of sequencing costs implies a need for algorithms able to process increasing amounts of generated data in reasonable time.

Results
We present Whisper, an accurate and high-performant mapping tool, based on the idea of sorting reads and then mapping them against suffix arrays for the reference genome and its reverse complement. Employing task and data parallelism as well as storing temporary data on disk result in superior time efficiency at reasonable memory requirements. Whisper excels at large NGS read collections, in particular Illumina reads with typical WGS coverage. The experiments with real data indicate that our solution works in about 15% of the time needed by the well-known BWA-MEM and Bowtie2 tools at a comparable accuracy, validated in a variant calling pipeline.

Availability and implementation
Whisper is available for free from https://github.com/refresh-bio/Whisper or http://sun.aei.polsl.pl/REFRESH/Whisper/.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Role of the Human Auditory Corticostriatal Network in Speech Learning
Authors: Feng Gangyi , Yi Han Gyol , Chandrasekaran Bharath 
Published: November 2018

Abstract
We establish a mechanistic account of how the mature human brain functionally reorganizes to acquire and represent new speech sounds. Native speakers of English learned to categorize Mandarin lexical tone categories produced by multiple talkers using trial-by-trial feedback. We hypothesized that the corticostriatal system is a key intermediary in mediating temporal lobe plasticity and the acquisition of new speech categories in adulthood. We conducted a functional magnetic resonance imaging experiment in which participants underwent a sound-to-category mapping task. Diffusion tensor imaging data were collected, and probabilistic fiber tracking analysis was employed to assay the auditory corticostriatal pathways. Multivariate pattern analysis showed that talker-invariant novel tone category representations emerged in the left superior temporal gyrus (LSTG) within a few hundred training trials. Univariate analysis showed that the putamen, a subregion of the striatum, was sensitive to positive feedback in correctly categorized trials. With learning, functional coupling between the putamen and LSTG increased during error processing. Furthermore, fiber tractography demonstrated robust structural connectivity between the feedback-sensitive striatal regions and the LSTG regions that represent the newly learned tone categories. Our convergent findings highlight a critical role for the auditory corticostriatal circuitry in mediating the acquisition of new speech categories.
MYH9-related disorders display heterogeneous kidney involvement and outcome
Authors: Tabibzadeh Nahid , Fleury Dominique , Labatut Delphine , Bridoux Frank , Lionet Arnaud , Jourde-Chiche Noémie , Vrtovsnik François , Schlegel Nicole , Vanhille Philippe 
Published: November 2018

AbstractBackgroundMYH9-related diseases (MYH9-RD) are autosomal dominant disorders caused by mutations of the MYH9 gene encoding the non-muscle myosin heavy chain IIA. They are characterized by congenital thrombocytopenia, giant platelets and leucocyte inclusions. Hearing impairment, pre-senile cataract and nephropathy can also occur. We aimed to evaluate renal involvement and outcome in MYH9-RD patients followed-up by nephrologists.MethodsWe conducted a retrospective multicentre observational study of 13 patients among 9 families with MYH9 mutation diagnosed by genetic testing and immunofluorescence assay referred to nephrologists.ResultsAt initial referral, median age was 30 (range 14–76) years. Median estimated glomerular filtration rate was 66 mL/min/1.73 m2 (0–141) and two patients had already end-stage renal disease (ESRD). Renal presentation associated proteinuria (n = 12), haematuria (n = 6) and hypertension (n = 6). Three patients developed a rapid onset ESRD whereas five others had a relatively stable kidney function over a 3-year median follow-up (1–34). Extra-renal features varied widely, with hearing impairment in six patients, cataract in two and mild liver dysfunction in seven. Thrombocytopenia existed at referral in 11 patients. Time to diagnosis varied from 0 to 29 years (median 3 years). Initial diagnoses such as idiopathic thrombocytopenic purpura (n = 4) and focal segmental glomerulosclerosis (n = 1) led to corticosteroid administration (n = 4), intravenous immunoglobulins (n = 3), cyclophosphamide (n = 1) and splenectomy (n = 1).ConclusionsRenal involvement and outcome in MYH9-RD are heterogeneous. The diagnosis is often delayed and misdiagnoses can lead to unnecessary treatments. MYH9-RD should be considered in any patient with glomerular involvement associated with a low or slightly decreased platelet count and/or hearing loss and liver dysfunction.
Polynomial Factorization Statistics and Point Configurations in ℝ3
Authors: Hyde Trevor 
Published: November 2018

Abstract
We use combinatorial methods to relate the expected values of polynomial factorization statistics over $\mathbb{F}_q$ to the cohomology of ordered configurations in $\mathbb{R}^3$ as a representation of the symmetric group. Our method gives a new proof of the twisted Grothendieck–Lefschetz formula for squarefree polynomial factorization statistics of Church, Ellenberg, and Farb.