bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of Thyroid Deficiency on Adiponectin, Leptin, and Metabolic Status in Visceral Obesity: A Cross-Sectional Study
Authors: Lozanov Lachezar , Gorcheva Desislava , Lozanov Bojan , Argirova Radka , Koleva Veselina , Kostova Boyka , Borisov Radoslav , Nedeva Mariana 
Published: July 2017

AbstractHypothyroidism results in disturbances of metabolism influencing many regulatory systems and active molecules as adipocytokines. Objective of the study was to investigate leptin and adiponectin in patients with visceral obesity and hypothyroidism in relation to metabolic status, insulin resistance and systemic inflammation. A total of 118 patients (59 hypothyroid and 59 euthyroid) were enrolled divided into four age-matched groups according to body wеight (BMI) and thyroid function. Laboratory panel includes TSH, FT4, FT3 (CMIA), adiponectin and leptin (ELISA), IL- 6 (ECLIA), CRP, insulin, glucose, apolipoprotein B and lipoprotein (a) - Lp(a). Hypothyroid patients revealed significant positive correlations of TSH, adiponectin and Lp(a). Their medians of 10.4 mU/l, 12.5 µg/ml and 116.3 mg/l respectively were significantly higher than in euthyroid patients- 1.5 mU/l, 6.26 µg/ml and 32.0 mU/l (p < 0.0001). Leptin in both obese groups was significantly higher than in patients with normal weight. Leptin in hypothyroid patients was lower but not significant to euthyroid ones (9.7 ng/ml vs 13.4 ng/ml respectively, p = 0.16), correlated negatively to TSH and positively to CRP, IL-6, ApoB, Lp(a) and BMI. HOMA-IR and serum insulin at 120 min in OGTT were significantly higher in hypothyroid than in euthyroid patients independent of BMI (p < 0.001). Adiponectin, insulin resistance and chronic inflammation indices in hypothyroid patients correlated positively to TSH, BMI and atherogenic lipoproteins subclasses ApoB/Lp(a). Increased adiponectin in thyroid deficiency could be due to secondary resistance of adiponectin receptors or appeared as a compensatory pathogenetic factor in hypothyroidism.
The influence of surface potential on the optical switching of spiropyran self assembled monolayers
Authors: Garling Tobias , Tong Yujin , Darwish Tamim A , Wolf Martin , Campen R Kramer 
Published: July 2017

Abstract
Surfaces whose macroscopic properties can be switched by light are potentially useful in a wide variety of applications. One such promising application is electrochemical sensors that can be gated by optically switching the electrode on or off. One way to make such a switchable electrode is by depositing a self-assembled monolayer (SAM) of bistable, optically switchable molecules onto an electrode surface. Quantitative application of any such sensor requires understanding how changes in interfacial field affect the composition of photostationary states, i.e. how does electrode potential affect the extent to which the electrode is on or off when irradiated, and the structure of the SAM. Here we address these questions for a SAM of a 6-nitro-substituted spiro[2H-1-benzopyran-2,2’-indoline] covalently attached through a dithiolane linker to an Au electrode immersed in a 0.1 M solution of Tetramethylammonium hexafluorophosphate in Acetonitrile using interface-specific vibrational spectroscopy. We find that in the absence of irradiation, when the SAM is dominated by the closed spiropyran form, variations in potential of 1 V have little effect on spiropyran relative stability. In contrast, under UV irradiation small changes in potential can have dramatic effects: changes in potential of 0.2 V can completely destabilize the open merocyanine form of the SAM relative to the spiropyran and dramatically change the chromophore orientation. Quantitatively accounting for these effects is necessary to employ this, or any other optically switchable bistable chromophore, in electrochemical applications.
PySeqLab: an open source Python package for sequence labeling and segmentation
Authors: Allam Ahmed , Krauthammer Michael 
Published: July 2017

Abstract

Motivation
Text and genomic data are composed of sequential tokens, such as words and nucleotides that give rise to higher order syntactic constructs. In this work, we aim at providing a comprehensive Python library implementing conditional random fields (CRFs), a class of probabilistic graphical models, for robust prediction of these constructs from sequential data.

Results
Python Sequence Labeling (PySeqLab) is an open source package for performing supervised learning in structured prediction tasks. It implements CRFs models, that is discriminative models from (i) first-order to higher-order linear-chain CRFs, and from (ii) first-order to higher-order semi-Markov CRFs (semi-CRFs). Moreover, it provides multiple learning algorithms for estimating model parameters such as (i) stochastic gradient descent (SGD) and its multiple variations, (ii) structured perceptron with multiple averaging schemes supporting exact and inexact search using ‘violation-fixing’ framework, (iii) search-based probabilistic online learning algorithm (SAPO) and (iv) an interface for Broyden–Fletcher–Goldfarb–Shanno (BFGS) and the limited-memory BFGS algorithms. Viterbi and Viterbi A* are used for inference and decoding of sequences. Using PySeqLab, we built models (classifiers) and evaluated their performance in three different domains: (i) biomedical Natural language processing (NLP), (ii) predictive DNA sequence analysis and (iii) Human activity recognition (HAR). State-of-the-art performance comparable to machine-learning based systems was achieved in the three domains without feature engineering or the use of knowledge sources.

Availability and implementation
PySeqLab is available through https://bitbucket.org/A_2/pyseqlab with tutorials and documentation.

Supplementary information
Supplementary data are available at Bioinformatics online.
Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies
Authors: Wang Meng , Ji Zhanglong , Wang Shuang , Kim Jihoon , Yang Hai , Jiang Xiaoqian , Ohno-Machado Lucila 
Published: July 2017

Abstract

Motivation
Inappropriate disclosure of human genomes may put the privacy of study subjects and of their family members at risk. Existing privacy-preserving mechanisms for Genome-Wide Association Studies (GWAS) mainly focus on protecting individual information in case–control studies. Protecting privacy in family-based studies is more difficult. The transmission disequilibrium test (TDT) is a powerful family-based association test employed in many rare disease studies. It gathers information about families (most frequently involving parents, affected children and their siblings). It is important to develop privacy-preserving approaches to disclose TDT statistics with a guarantee that the risk of family ‘re-identification’ stays below a pre-specified risk threshold. ‘Re-identification’ in this context means that an attacker can infer that the presence of a family in a study.

Methods
In the context of protecting family-level privacy, we developed and evaluated a suite of differentially private (DP) mechanisms for TDT. They include Laplace mechanisms based on the TDT test statistic, P-values, projected P-values and exponential mechanisms based on the TDT test statistic and the shortest Hamming distance (SHD) score.

Results
Using simulation studies with a small cohort and a large one, we showed that that the exponential mechanism based on the SHD score preserves the highest utility and privacy among all proposed DP methods. We provide a guideline on applying our DP TDT in a real dataset in analyzing Kawasaki disease with 187 families and 906 SNPs. There are some limitations, including: (1) the performance of our implementation is slow for real-time results generation and (2) handling missing data is still challenging.

Availability and implementation
The software dpTDT is available in https://github.com/mwgrassgreen/dpTDT.

Supplementary information
Supplementary data are available at Bioinformatics online.
New Genes and Functional Innovation in Mammals
Authors: Villanueva-Cañas José Luis , Ruiz-Orera Jorge , Agea M. Isabel , Gallo Maria , Andreu David , Albà M. Mar 
Published: July 2017

Abstract
The birth of genes that encode new protein sequences is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected for. To address these questions, we have obtained a large collection of mammalian-specific gene families that lack homologues in other eukaryotic groups. We have combined gene annotations and de novo transcript assemblies from 30 different mammalian species, obtaining ∼6,000 gene families. In general, the proteins in mammalian-specific gene families tend to be short and depleted in aromatic and negatively charged residues. Proteins which arose early in mammalian evolution include milk and skin polypeptides, immune response components, and proteins involved in reproduction. In contrast, the functions of proteins which have a more recent origin remain largely unknown, despite the fact that these proteins also have extensive proteomics support. We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.
Parameter Spaces for Algebraic Equivalence
Authors: Achter Jeffrey D , Casalaina-Martin Sebastian , Vial Charles 
Published: July 2017

Abstract
A cycle is algebraically trivial if it can be exhibited as the difference of two fibers in a family of cycles parameterized by a smooth integral scheme. Over an algebraically closed field, it is a result of Weil that it suffices to consider families of cycles parameterized by curves, or by abelian varieties. In this article, we extend these results to arbitrary base fields. The strengthening of these results turns out to be a key step in our work elsewhere extending Murre’s results on algebraic representatives for varieties over algebraically closed fields to arbitrary perfect fields.
Tearing Spacetime Asunder
Authors: Callender Craig 
Published: July 2017

The physicist Hermann Minkowski famously claimed that relativity implies that space and time are doomed to fade away into mere shadows. It therefore may come as a surprise that relativistic spacetime is often decomposed into “time” and “space” in so-called “3 + 1” formulations of relativity. How should we regard these times? Are they hospitable to manifest time? This chapter adopts the perspective that relativity is still a “live” theory under development, so a distinguished time could emerge. However, such a time is unlikely to live up to what we want in manifest time.
Case Series: Keratolimbal Allograft as a Patch Graft for Glaucoma Drainage Devices
Authors: Ahmed Sarah F. , Schmutz Mason , Mosaed Sameh 
Published: July 2017

Purpose:
Tube exposure remains one of the most common complications after glaucoma drainage device (GDD) implantation, despite various types of patch grafts available today. We present a 4 patient case series following the effectivity of the keratolimbal allograft (KLAL) as a patch graft for cases of tube exposure. Given its inherent population of stem cells, our hypothesis was that this highly replicative, biological tissue would provide an adequate means of glaucoma tube coverage. The subset of patients chosen for the KLAL patch graft all had a history of abnormally scarred conjunctiva or thin sclera. The aim of utilizing the KLAL patch with its associated donor conjunctival and scleral ring was also to provide additional reinforcement and adequate tube coverage in the setting of compromised native tissue.

Observations:
Four patients comprised of 2 males and 2 females with a minimum postoperative period of 12 months. All GDDs were initially implanted with a limbal-based incision using either Ahmed glaucoma valve or Baerveldt drainage implant. Three of the 4 patients received the KLAL patch graft after tube exposure with scleral patch graft and 1 patient received KLAL as the primary graft during initial tube placement.

Conclusions:
Two of the 4 eyes experienced tube re-exposure postoperatively at 2 and 3 months, respectively. Both of these cases had a history of prior tube exposure after scleral patch graft and both were tubes placed in the pars plana. Interestingly, the patients with failed grafts were younger with a history of more ocular surgeries as compared with the patients with graft viable eyes.

Relevance:
Through our case series, we found that the KLAL utilized as a patch graft over GDD tubes has the potential for favorable outcomes in certain subtypes of eyes. Although further large scale investigation will be necessary to better define the risk factors associated with graft failure, proving the graft’s viability is a crucial first step.
Treatment Minimization in Older Patients With Early-Stage Breast Cancer
Authors: Hansen Tara M. , Zellars Richard C. 
Published: July 2017

Abstract
The management of early-stage breast cancer in older patients is complex and requires a careful balance of the risk of cancer death with the competing risks of comorbidities and treatment-related toxicity in women with largely favorable disease. As the US population continues to age, oncologists will increasingly encounter this clinical challenge. Several strategies involving each core component of breast cancer therapy have been investigated to minimize treatment in these patients while still maintaining acceptable outcomes. These include omission of primary tumor resection, surgical axillary evaluation, systemic chemotherapy, and/or radiotherapy, as well as reduction in radiotherapy treatment volume (partial breast irradiation) or total treatment time (hypofractionation). We review these strategies and the literature supporting their use, as well as future directions for treatment minimization.
Managing Cancer Pain in Older Adults
Authors: Guerard Emily J. , Cleary James F. 
Published: July 2017

Abstract
Managing cancer pain in older adults can be complex and challenging. Understanding the unique needs of older patients with cancer is important to safe and effective pain management. The goals of this review are to discuss the assessment of older adults with cancer-related pain, treatment of cancer pain, and adverse effects or potential risks from treatment that are unique to older patients. A detailed pain assessment and when possible utilizing the geriatric assessment are vital to developing a cancer pain management plan. The geriatric assessment can help clinicians uncover problems not routinely assessed in the standard oncologic evaluation. Opioid pain medications are safe and effective for older adults with cancer pain as long as these medications are closely monitored and titrated slowly. In addition to the well-known adverse effects of opioid medications, clinicians need to be aware of the unique risks in older adults, which could include delirium, polypharmacy, and falls.
The Metabolopathy of Tissue Injury, Hemorrhagic Shock, and Resuscitation in a Rat Model
Authors: Slaughter Anne L. , Nunns Geoffrey R. , D’Alessandro Angelo , Banerjee Anirban , Hansen Kirk C. , Moore Ernest E. , Silliman Christopher C. , Nemkov Travis , Moore Hunter B. , Fragoso Miguel , Leasia Kiara , Peltz Erik D. 
Published: July 2017

ABSTRACT

Introduction:
The metabolic consequences of trauma induce significant clinical pathology. In this study, we evaluate the independent, metabolic contributions of tissue injury (TI) and combined tissue injury and hemorrhagic shock (TI/HS) using mass spectrometry (MS) metabolomics in a controlled animal model of critical injury.

Methods:
Sprague–Dawley rats (n = 14) underwent TI alone or TI/HS, followed by resuscitation with normal saline and shed blood. Plasma was collected (baseline, post-laparotomy, post-HS, post-resuscitation) for ultra-high pressure liquid chromatography MS-metabolomics. Repeated-measures ANOVA with Tukey multiple column comparison test compared the fold change of metabolite concentration among the animal groups at corresponding time points.

Results:
Four hundred forty metabolites were identified. TI alone did not change the metabolite levels versus baseline. TI/HS induced changes in metabolites from glycolysis, the tricarboxylic acid cycle, the pentose phosphate, fatty acid and glutathione homeostasis pathways, sulfur metabolism, and urea cycle versus TI alone. Following resuscitation many metabolites normalized to TI alone levels, including lactate, most tri-carboxylic acid metabolites, most urea cycle metabolites, glutathione disulfide, and some metabolites from both the pentose phosphate pathway and sulfur metabolism.

Conclusions:
Significant changes occur immediately following TI/HS versus TI alone. These metabolic changes are not explained by dilution as a number of metabolites remained unchanged or even increased following resuscitation. The differential metabolic changes resulting from TI alone and TI/HS provide foundation for future investigations severe injury in humans, where TI and HS are often concurrent. This investigation provides a foundation to evaluate metabolic-related outcomes and design-targeted resuscitation strategies.
Genetics and genomics of social behaviour in a chicken model
Authors: Johnsson M. , Henriksen R. , Fogelholm J. , Höglund A. , Jensen P. , Wright D. 
Published: July 2017

ABSTRACTThe identification of genes affecting behaviour can be problematic, yet their identification allows a raft of possibilities. Sociality and social behaviour can have multiple definitions, though at its core it is the desire to seek contact with con- or hetero-specifics. The identification of genes affecting sociality can therefore give insights into the maintenance and establishment of sociality. In this study we used the combination of an advanced intercross between wild and domestic chickens with a combined QTL and eQTL genetical genomics approach to identify genes for social reinstatement (SR) behaviour. A total of 24 SR QTL were identified and overlaid with over 600 eQTL obtained from the same birds using hypothalamus tissue. Correlations between overlapping QTL and eQTL indicated 5 strong candidate genes, with the geneTTRAPbeing strongly significantly correlated with multiple aspects of SR behaviour, as well as possessing a highly significant eQTL. The distribution of eQTL can also indicate the genetic mechanisms underlying domestication itself. Multiple eQTL were found to in discrete clusters, however tests for pleiotropy show that these blocks were primarily linked in origin. This suggests that clustered genetic modules, rather than pure pleiotropy (as hypothesised by the neural crest theory) appears to be driving domestication in the chicken.
Polygenic Risk Score of Sporadic late Onset Alzheimer Disease Reveals a Shared Architecture with the Familial and Early Onset Forms
Authors: Del-Aguila Jorge L , Saef Benjamin , Black Kathleen , Fernandez Maria Victoria , Budde John , Ibanez Laura , Kapoor Manav , Tosto Giuseppe , Mayeux Richard P , Holtzman David M , Fagan Anne M. , Morris John C , Bateman Randall J. , Goate Alison ,   the Dominantly Inherited Alzheimer Network (DIAN), Disease Neuroimaging Initiative (ADNI),   the NIA-LOAD family study, Cruchaga Carlos , Harari Oscar 
Published: July 2017

AbstractObjective:To determine whether the genetic architecture of sporadic late-onset Alzheimer’s Disease (sLOAD) has an effect on familial late-onset AD (fLOAD), sporadic early-onset (sEOAD) and autosomal dominant early-onset (eADAD).Methods:Polygenic risk scores (PRS) were constructed using previously identified 21 genome-wide significant loci for LOAD risk.Results:We found that there is an overlap in the genetic architecture among sEOAD, fLOAD, and sLOAD. sEOAD showed the highest odds for the PRS (OR=2.27; p=1.29×10-7), followed by fLOAD (OR=1.75; p=1.12×10-7) and sLOAD (OR=1.40; p=1.21×10-3). PRS is associated with cerebrospinal fluid ptau181-Aβ42on eADAD.Conclusion:Our analysis confirms that the genetic factors identified for sLOAD also modulate risk in fLOAD and sEOAD cohorts. Furthermore, our results suggest that the burden of these risk variants is associated with familial clustering and earlier-onset of AD. Although these variants are not associated with risk in the eADAD, they may be modulating age at onset.
Optimization of Alginante-poly-L-lysine Microencapsules Strength by Box-Behnken Model for CHO cells Culture in Stirred Tank Bioreactor
Authors: Wang Yu , Li Na , Sun Dongsheng , He Shengnan , Mou Lisha 
Published: July 2017

Summary statementBox-Behnken model is an efficient method to optimized process conditions of microencapsules strength for long-term cell culture, promotes CHO cells viability and protein production in a stirred tank bioreactor.ABSTRACTCell microencapsulation technology has been proved to be a valuable technology in the fields of large-scale cell culture. It is important to accurately construct the microcapsule membranes with desired properties including a certain thickness suitable for cell growth, and maximum strength for the stability of microencapsules. As single factor experiments are time-consuming to obtain the desired membrane preparation conditions, Box-Behnken model was used to investigate the interactions among reaction conditions, predict the optimized reaction conditions for given purpose, that was membrane with maximum strength and desired thickness for microencapsulated cell culture. Significant values of R2in this study indicated the model theoretical values are very close to the measured values. Based on the desired membrane thickness, the process of maximum strength was optimized, and the prediction agreement of measured value and model theoretical value was 91.11%. The optimized microencapsules with maximum strength and 15 μm membrane thickness promote CHO cells viability and protein production in stirred tank bioreactor. The result shows that Box-Behnken model is an efficient method to optimized process conditions of microencapsules strength for long-term cell culture.
Collaborative environmental DNA sampling from petal surfaces of flowering cherryCerasus ×- yedoensis'Somei-yoshino' across the Japanese archipelago
Authors: Ohta Tazro , Kawashima Takeshi , Shinozaki Natsuko O. , Dobashi Akito , Hiraoka Satoshi , Hoshino Tatsuhiko , Kanno Keiichi , Kataoka Takafumi , Kawashima Shuichi , Matsui Motomu , Nemoto Wataru , Nishijima Suguru , Suganuma Natsuki , Suzuki Haruo , Taguchi Y-h. , Takenaka Yoichi , Tanigawa Yosuke , Tsuneyoshi Momoka , Yoshitake Kazutoshi , Sato Yukuto , Yamashita Riu , Arakawa Kazuharu , Iwasaki Wataru 
Published: July 2017

AbstractRecent studies have shown that environmental DNA is found almost everywhere. Flower petal surfaces are an attractive tissue to use for investigation of the dispersal of environmental DNA in nature as they are isolated from the external environment until the bud opens and only then can the petal surface accumulate environmental DNA. Here, we performed a crowdsourced experiment, the “Ohanami Project”, to obtain environmental DNA samples from petal surfaces ofCerasus × yedoensis‘Somei-yoshino’ across the Japanese archipelago during spring 2015.C. × yedoensisis the most popular garden cherry species in Japan and clones of this cultivar bloom simultaneously every spring. Data collection spanned almost every prefecture and totaled 577 DNA samples from 149 collaborators. Preliminary amplicon-sequencing analysis showed the rapid attachment of environmental DNA onto the petal surfaces. Notably, we found DNA of other common plant species in samples obtained across a wide distribution; this DNA likely originated from pollen of the Japanese cedar. Our analysis supports our belief that petal surfaces after blossoming are a promising target to reveal the dynamics of environmental DNA in nature. The success of our experiment also shows that crowdsourced environmental DNA analyses have considerable value in ecological studies.