bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems
Authors: Ushakov Kathy , Koffler-Brill Tal , Rom Aviv , Perl Kobi , Ulitsky Igor , Avraham Karen B. 
Published: August 2017

AbstractMammalian genomes encode multiple layers of regulation, including a class of RNA molecules known as long non-coding RNAs (lncRNAs). These are >200 nucleotides in length and similar to mRNAs, they are capped, polyadenylated, and spliced. In contrast to mRNAs, lncRNAs are less abundant and have higher tissue specificity, and have been linked to development, epigenetic processes, and disease. However, little is known about lncRNA function in the auditory and vestibular systems, or how they play a role in deafness and vestibular dysfunction. To help address this need, we performed a whole-genome identification of lncRNAs using RNA-seq at two developmental stages of the mouse inner ear sensory epithelium of the cochlea and vestibule. We identified 3,239 lncRNA genes, most of which were intergenic (lincRNAs) and 721 are novel. We examined temporal and tissue specificity by analyzing the developmental profiles on embryonic day 16.5 and at birth. The spatial and temporal patterns of three lncRNAs, two of which are in proximity to genes associated with hearing and deafness, were explored further. Our findings indicate that lncRNAs are prevalent in the sensory epithelium of the mouse inner ear and are likely to play key roles in regulating critical pathways for hearing and balance.
Suspected limited mobility of a Middle Pleistocene woman from Southern Italy: strontium isotopes of a human deciduous tooth
Authors: Lugli Federico , Cipriani Anna , Arnaud Julie , Arzarello Marta , Peretto Carlo , Benazzi Stefano 
Published: August 2017

AbstractWe present the Sr isotopic composition of enamel of the most ancient deciduous tooth ever discovered in Italy to assess human mobility in Middle Pleistocene. Reconstructing ancient mobility is crucial for understanding human strategy at exploiting temporally and spatially patchy resources, with most studies focusing on indirect evidences, ultimately affecting our interpretation on hominin territoriality and energetic costs invested by hominin groups. Here, we use the high spatial resolution and micro-destructivity options offered by the Laser Ablation Multi-Collector Inductively Coupled Plasma Mass Spectrometry technique, to determine the 87Sr/ 86Sr intra-tooth variability of a human deciduous incisor from the Middle Pleistocene layers of the Isernia La Pineta site (Italy). We compared these data with the Sr isotopic signature of local micro-mammals, the broadest home-range of the macro-mammals and with modern plant samples. Our study reveals that while macro-mammals have possibly migrated through the landscape for up to 50 km, the pregnant woman from Isernia was probably local, given that the isotopic ratio of the enamel falls within the local range and is comparable with the signature of the local plants in a radius of 10 km. This is the first case study of Sr isotopic composition determination in such ancient deciduous tooth.
Isothermal Amplification of Long, Discrete DNA Fragments Facilitated by Single-Stranded Binding Protein
Authors: Zhang Yinhua , Tanner Nathan A. 
Published: August 2017

AbstractIsothermal amplification methods for detection of DNA and RNA targets have expanded significantly in recent years, promising a new wave of simple and rapid molecular diagnostics. Current isothermal methods result in the generation of short fragments (<150 base pairs) or highly branched long DNA products. Here we report the amplification of discrete target fragments of several kilobases at 37 °C from both double- and single-stranded circular template DNA using specific primer pairs. In contrast to existing methods, this amplification requires only the single-stranded DNA-binding protein gp32 from bacteriophage T4 and a strand-displacing DNA polymerase. In addition to the discrete amplicon products, this method also produces higher molecular weight products consisting of multiple repeated copies of the amplicon and template DNA. We demonstrate that two features of gp32 enable this amplification: a facilitation of primer strand invasion into double-stranded DNA, and a suppression of non-homologous primer annealing and nonspecific amplification. The ability presented here to produce long, discrete DNA products in an isothermal reaction extends the scope of isothermal amplification to enable more useful applications of these promising methods.
MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis
Authors: Isom Georgia L. , Davies Nathaniel J. , Chong Zhi-Soon , Bryant Jack A. , Jamshad Mohammed , Sharif Maria , Cunningham Adam F. , Knowles Timothy J. , Chng Shu-Sin , Cole Jeffrey A. , Henderson Ian R. 
Published: August 2017

AbstractBacterial proteins with MCE domains were first described as being important for Mammalian Cell Entry. More recent evidence suggests they are components of lipid ABC transporters. In Escherichia coli, the single-domain protein MlaD is known to be part of an inner membrane transporter that is important for maintenance of outer membrane lipid asymmetry. Here we describe two multi MCE domain-containing proteins in Escherichia coli, PqiB and YebT, the latter of which is an orthologue of MAM-7 that was previously reported to be an outer membrane protein. We show that all three MCE domain-containing proteins localise to the inner membrane. Bioinformatic analyses revealed that MCE domains are widely distributed across bacterial phyla but multi MCE domain-containing proteins evolved in Proteobacteria from single-domain proteins. Mutants defective in mlaD, pqiAB and yebST were shown to have distinct but partially overlapping phenotypes, but the primary functions of PqiB and YebT differ from MlaD. Complementing our previous findings that all three proteins bind phospholipids, results presented here indicate that multi-domain proteins evolved in Proteobacteria for specific functions in maintaining cell envelope homeostasis.
Precise stacking of decellularized extracellular matrix based 3D cell-laden constructs by a 3D cell printing system equipped with heating modules
Authors: Ahn Geunseon , Min Kyung-Hyun , Kim Changhwan , Lee Jeong-Seok , Kang Donggu , Won Joo-Yun , Cho Dong-Woo , Kim Jun-Young , Jin Songwan , Yun Won-Soo , Shim Jin-Hyung 
Published: August 2017

AbstractThree-dimensional (3D) cell printing systems allow the controlled and precise deposition of multiple cells in 3D constructs. Hydrogel materials have been used extensively as printable bioinks owing to their ability to safely encapsulate living cells. However, hydrogel-based bioinks have drawbacks for cell printing, e.g. inappropriate crosslinking and liquid-like rheological properties, which hinder precise 3D shaping. Therefore, in this study, we investigated the influence of various factors (e.g. bioink concentration, viscosity, and extent of crosslinking) on cell printing and established a new 3D cell printing system equipped with heating modules for the precise stacking of decellularized extracellular matrix (dECM)-based 3D cell-laden constructs. Because the pH-adjusted bioink isolated from native tissue is safely gelled at 37 °C, our heating system facilitated the precise stacking of dECM bioinks by enabling simultaneous gelation during printing. We observed greater printability compared with that of a non-heating system. These results were confirmed by mechanical testing and 3D construct stacking analyses. We also confirmed that our heating system did not elicit negative effects, such as cell death, in the printed cells. Conclusively, these results hold promise for the application of 3D bioprinting to tissue engineering and drug development.
Distribution bias and biochemical characterization of TOP1MT single nucleotide variants
Authors: Zhang Hongliang , Seol Yeonee , Agama Keli , Neuman Keir C. , Pommier Yves 
Published: August 2017

AbstractMitochondrial topoisomerase I (TOP1MT) is a type IB topoisomerase encoded in the nucleus of vertebrate cells. In contrast to the other five human topoisomerases, TOP1MT possesses two high frequency single nucleotide variants (SNVs), rs11544484 (V256I, Minor Allele Frequency = 0.27) and rs2293925 (R525W, MAF = 0.45), which tend to be mutually exclusive across different human ethnic groups and even more clearly in a cohort of 129 US patients with breast cancer and in the NCI-60 cancer cell lines. We expressed these two TOP1MT variants and the double-variant (V256I-R525W) as recombinant proteins, as well as a less common variant E168G (rs200673353, MAF = 0.001), and studied their biochemical properties by magnetic tweezers-based supercoil relaxation and classical DNA relaxation assays. Variants showed reduced DNA relaxation activities, especially the V256I variant towards positively supercoiled DNA. We also found that the V256I variant was enriched to MAF = 0.64 in NCI-60 lung carcinoma cell lines, whereas the TOP1MT R525W was enriched to MAF = 0.65 in the NCI-60 melanoma cell lines. Moreover, TOP1MT expression correlated with the 256 variants in the NCI-60 lung carcinoma cell lines, valine with high expression and isoleucine with low expression. Our results are discussed in the context of evolution between the nuclear and mitochondrial topoisomerases and potential cancer predisposition.
Brazilian Women's Health after 65 Years of Age
Authors: Fonseca Angela Maggio da , Bagnoli Vicente Renato , Massabki Josefina Odete Polak , Arie Wilson Maça Yuki , Azevedo Raymundo Soares , Soares Jr José Maria , Baracat Edmund C. 
Published: August 2017

Purpose The aim of this study was to evaluate the health aspects of Brazilian women older than 65 years of age.
Design This was a retrospective study that included 1,001 Brazilian women cared for in the gynecological geriatric outpatient office of our institution. We report a cross-sectional analysis of female adults aged over 65 years, including data on demographics, clinical symptoms such as vasomotor symptoms, associated morbidities, physical examination and sexual intercourse. We used the chi-squared test to assess the data.
Results The age of the patients on their first clinic visit ranged from 65 to 98 years, with a mean age of 68.56 ± 4.47 years; their mean age at the time of natural menopause was 48.76 ± 5.07 years. The most frequent clinical symptoms reported during the analyzed period were hot flashes (n = 188), followed by arthropathy, asthenia, and dry vagina. The most frequent associated morbidities after 65 years of age were systemic arterial hypertension, gastrointestinal disturbance, diabetes mellitus, and depression, among others. The assessment of the body mass index (BMI) found decreases in BMI with increased age. At the time of the visit, 78 patients reported sexual intercourse. The majority of women reporting sexual intercourse (89.75%, n =  70) were between 65 and 69 years of age, 8.97% (n = 7) were between 70 and 74 years of age, and only 1.28% (n = 1) of those were aged older than 75 years.
Conclusions Our findings suggested that vasomotor symptoms can persist after 65 years of age. There was a significant decrease in sexual intercourse with increased age. The cardiovascular disturbances in our study are health concerns in these women.
Patient with Recurrent Glioblastoma Responding Favorably to Ketogenic Diet Combined with Intranasal Delivery of Perillyl Alcohol: A Case Report and Literature Review
Authors: Santos Juliana , Cruz Wanise , Schönthal Axel , Salazar Marcela , Fontes Cristina , Quirico-Santos Thereza , Fonseca Clovis 
Published: August 2017

Introduction Monoterpene perillyl alcohol (POH) is cytotoxic to temozolomide-resistant glioma cells, regardless of its O6-methylguanine-methyltransferase (MGMT) promoter methylation status. Moreover, adherence to a ketogenic diet (KD) produced successful outcomes in preclinical and clinical studies in the glioma setting.
Case Presentation A 54-year-old Caucasian man had a confirmed diagnosis of refractory glioblastoma multiforme (GBM). The immunohistochemical evaluation was negative for methylation, and failed to detect mutations in the isocitrate dehydrogenase (IDH) 1 and 2 genes. In January 2016, the patient was enrolled in a clinical trial combining daily intranasal delivery of POH in combination with a KD. The KD was administered concomitantly with inhalation of POH (55 mg, 4 times a day) in an uninterrupted administration schedule for 3 months.
Results The combination treatment was well-tolerated. The nutritional status and anthropometric measurements of the patient were measured. Adherence to the KD was confirmed by measuring the levels of ketone bodies in the urine. Throughout the treatment, a reduced frequency of seizures was observed. After three months of adherence to the treatment, the patient presented with weight loss, reduced body fat, increased water retention, and a slight increase in bone and muscle mass. A follow-up magnetic resonance imaging (MRI) scan after 3 months of treatment revealed marked reduction of the enhancing lesion.
Conclusion Intranasal delivery of POH combined with concomitant adherence to a KD appeared to have a beneficial therapeutic effect in a patient with recurrent GBM. Further studies are needed to evaluate the efficacy of this therapeutic strategy in a larger cohort of treatment-refractory GBM patients.
Performance Factors in a Mountain Ultramarathon
Authors: Balducci Pascal , Clémençon Michel , Trama Robin , Blache Yoann , Hautier Christophe 
Published: August 2017

AbstractThis study aimed to determine mountain ultra-marathon (MUM) performance factors in a large group of endurance mountain runners. Maximal aerobic speed (MAS) was assessed one week prior to the MUM. The level and graded (10%) energy cost of running, stiffness, knee extensors force (KEf), and jump height on a counter movement jump (CMJ) were measured in 24 male ultra runners before (pre) and immediately after (post) the Interlacs Trail (75 km and 3 930/3 700 m d+/d−). Performance time was correlated with MAS (r=− 0.74, p<0.001), fraction of MAS (FMAS) sustained (r=− 0.89, p<0.001), KEf (r=− 0.51, p<0.05), and KEf loss (r=− 0.51, p<0.05). A multiple regression analysis was performed using performance time in minutes (T) and the calculated individual characteristics, resulting in T=− 11.852×FMAS−37.195×MAS−0.118×KEf+2090.581 (R2=0.98, with 95% confidence interval). Contrary to expectations, performance was neither correlated to the level or uphill energy cost of running nor to the changes of these costs post-MUM. To perform in a MUM, training should take into account muscle strength of the KE, MAS and FMAS.
Osteopathische Therapie bei manifestem Diabetes Typ 2
Authors: Mahler Renate 
Published: August 2017

ZusammenfassungDer Diabetes Typ 2 ist eine derWohlstandserkrankungen unserer Zeit. In diesem Beitrag werden die pathophysiologischen Zusammenhänge und
Risikofaktoren dieser Erkrankung dargestellt. Osteopathische Behandlungsansätze werden unter Berücksichtigung anatomischer Gegebenheiten
erläutert und die besondere Bedeutung der ganzheitlichen Begleitung von betroffenen Patienten wird dargestellt.
Funktionelle Beschwerden des respiratorischen Systems
Authors: Junge Martin 
Published: August 2017

ZusammenfassungAlles nur heiße Luft? Mitnichten. Neben dem Herzschlag und der Verdauung ist die Fähigkeit zu atmen eine grundlegende Voraussetzung unseres
Lebens. Bleibt uns sprichwörtlich „die Luft weg", reagieren wir ganz natürlich und automatisch mit ängstlichen, mitunter sogar panischen
Zuständen.Eine veränderte Atmung und ein veränderter Atemablauf haben weitereichende Folgen für den Rest des Körpers und das Wohlbefinden des
Patienten. Die wachsende Zahl von Patienten mit Asthma stellt eine große Herausforderung für Ärzte und Therapeuten dar. Eine dauerhafte
Einnahme von Medikamenten ist ebenfalls mit Folgen für den gesamten Körper verbunden; osteopathische Methoden in die Therapie zu
integrieren, ist deshalb sinnvoll.Dieser Artikel soll die Zusammenhänge zwischen dem parietalen und respiratorischen System darstellen und mögliche Folgen einer veränderten
Atmung aufzeigen. Ebenso werden vegetative Einflüsse und Behandlungsansätze einer osteopathischen Intervention eingebunden, nachdem die
Physiologie der Atmung und die Pathophysiologie des Asthma bronchiale beleuchtet wurden.
Prediction of delayed retention of antibodies in hydrophobic interaction chromatography from sequence using machine learning
Authors: Jain Tushar , Boland Todd , Lilov Asparouh , Burnina Irina , Brown Michael , Xu Yingda , Vásquez Maximiliano 
Published: August 2017

AbstractMotivationThe hydrophobicity of a monoclonal antibody is an important biophysical property relevant for its developability into a therapeutic. In addition to characterizing heterogeneity, Hydrophobic Interaction Chromatography (HIC) is an assay that is often used to quantify the hydrophobicity of an antibody to assess downstream risks. Earlier studies have shown that retention times in this assay can be correlated to amino-acid or atomic propensities weighted by the surface areas obtained from protein 3-dimensional structures. The goal of this study is to develop models to enable prediction of delayed HIC retention times directly from sequence.ResultsWe utilize the randomforest machine learning approach to estimate the surface exposure of amino-acid side-chains in the variable region directly from the antibody sequence. We obtain mean-absolute errors of 4.6% for the prediction of surface exposure. Using experimental HIC data along with the estimated surface areas, we derive an amino-acid propensity scale that enables prediction of antibodies likely to have delayed retention times in the assay. We achieve a cross-validation Area Under Curve of 0.85 for the Receiver Operating Characteristic curve of our model. The low computational expense and high accuracy of this approach enables real-time assessment of hydrophobic character to enable prioritization of antibodies during the discovery process and rational engineering to reduce hydrophobic liabilities.Availability and implementationStructure data, aligned sequences, experimental data and prediction scores for test-cases, and R scripts used in this work are provided as part of the Supplementary Material.Supplementary informationSupplementary data are available at Bioinformatics online.
Seroprevalence of Anti-polio Antibodies in Children From Polio High-risk Areas of Pakistan
Authors: Hussain Imtiaz , Mach Ondrej , Habib Atif , Bhatti Zaid , Suhag Zamir , Oberste M. Steven , Weldon William C. , Sutter Roland W. , Soofi Sajid B. , Bhutta Zulfiqar A. 
Published: August 2017

Background:
Pakistan is one of the 3 remaining wild poliovirus endemic countries. We collected sera from children to assess the prevalence of poliovirus antibodies in selected high-risk areas for poliovirus transmission.

Methods:
Children in 2 age groups (6–11 and 36–48 months) were randomly selected between November 2015 and March 2016 in 6 areas of Pakistan (Sindh Province: Karachi and Kashmore; Khyber Pakhtunkhwa Province: Peshawar, Bannu and Nowshera; Punjab Province: Faisalabad). After obtaining informed consent, basic demographic and vaccination history data were collected, 1 peripheral venipuncture was obtained, and assays to detect poliovirus (PV)–neutralizing antibodies were performed.

Results:
A total of 1301 children were enrolled and had peripheral blood drawn that analyzed. Study subjects were evenly distributed among survey sites and age groups. Anti-polio seroprevalence differed significantly among geographic areas (P < 0.001); in the 6–11 months group, it ranged between 89% and 98%, 58% and 95%, and 74% and 96% for PV serotypes 1, 2 and 3, respectively; in 36–48 months group, it ranged between 99% and 100%, 95% and 100%, and 92% and 100% for PV 1, 2, and 3, respectively. Having received inactivate poliovirus vaccine, malnourishment (stunting) and educational level of parents were found to be associated with presence of anti-polio antibodies.

Conclusion:
The polio eradication program achieved overall high serologic protection; however, immunity gaps in young children in the high polio risk areas remain. These gaps enable sustained circulation of wild poliovirus type 1, and pose risk for emergence of vaccine-derived polioviruses. Focusing on the lowest socioeconomic strata of society, where malnutrition is most prevalent, could accelerate poliovirus eradication.
Physics and Histologic Evaluation of Rotary, Ultrasonic, and Sonic Instruments
Authors: Ruga Emanuele , Amerio Ettore , Carbone Vincenzo , Volante Marco , Gandolfo Sergio 
Published: August 2017

Abstract
Rotary instruments (RIs) are the most commonly used to perform osteotomies in many fields of medicine. Owing to a new interest in performing a minimally invasive surgery, over last fifteen years new devices have been used in oral surgery such as ultrasonic instruments (UIs) and, lately, sonic instruments (SIs). Nowadays, bone preservation and regeneration are paramount in many clinical situations and, consequently, it is crucial to rely upon instruments, which cause the least tissue damage during the surgery. Concerning SIs, there is still few information about workload to be applied and related temperature increases; furthermore, there are no comparative in-vivo studies, which analyze the thermal and mechanical effects on bone. Thus, SIs have been compared with UIs and RIs in terms of heat generation, operating time, accuracy, and tissue damage. Decalcification and sectioning procedure resulted in no significant differences between the applied instruments in terms of bone damage. RIs resulted more efficient than UIs (P < 0.001), but demonstrated low accuracy (NRS 4.9), whereas SIs (P = 0.005) required more time to perform the osteotomy. The maximum temperature increase occurred in the ultrasonic group. Even though SI were the slowest, they have proved to be the most accurate (NRS 8.4) in comparison with UI (NRS 7.6) and RI (NRS 4.9). Within the limit of this study, sonic instruments could be considered a safe alternative to ultrasonic instruments.
Learning sequence patterns of AGO-sRNA affinity from high-throughput sequencing libraries to improvein silicofunctional small RNA detection and classification in plants
Authors: Morgado Lionel , Jansen Ritsert C. , Johannes Frank 
Published: August 2017

ABSTRACTThe loading of small RNA (sRNA) into Argonaute (AGO) complexes is a crucial step in all regulatory pathways identified so far in plants that depend on such non-coding sequences. Important transcriptional and post-transcriptional silencing mechanisms can be activated depending on the specific AGO protein to which sRNA bind. It is known that sRNA-AGO associations are at least partly encoded in the sRNA primary structure, but the sequence features that drive this association have not been fully explored. Here we train support vector machines (SVM) on sRNA sequencing data obtained from AGO-immunoprecipitation experiments to identify features that determine sRNA affinity to specific AGOs. Our SVM reveal that AGO affinity is strongly determined by complex k-mers in the 5’ and 3’ ends of sRNA, in addition to well-known features such as sRNA length and the base composition of the first nucleotide. Moreover, we find that these k-mers tend to overlap known transcription factor (TF) binding motifs, thus highlighting a close interplay between TF and sRNA-mediated transcriptional regulation. We embedded the learned SVM in a computational pipeline that can be used for de novo functional classification of sRNA sequences. This tool, called SAILS, is provided as a web portal accessible athttp://sails.eu.nu.