bluuebunny/crossref_metadata_2025_split huggingface dataset:
Charge neutralization in the active site of the catalytic trimer of aspartate transcarbamoylase promotes diverse structural changes
Authors: Endrizzi James A. , Beernink Peter T. 
Published: August 2017

AbstractA classical model for allosteric regulation of enzyme activity posits an equilibrium between inactive and active conformations. An alternative view is that allosteric activation is achieved by increasing the potential for conformational changes that are essential for catalysis. In the present study, substitution of a basic residue in the active site of the catalytic (C) trimer of aspartate transcarbamoylase with a non‐polar residue results in large interdomain hinge changes in the three chains of the trimer. One conformation is more open than the chains in both the wild‐type C trimer and the catalytic chains in the holoenzyme, the second is closed similar to the bisubstrate‐analog bound conformation and the third hinge angle is intermediate to the other two. The active‐site 240s loop conformation is very different between the most open and closed chains, and is disordered in the third chain, as in the holoenzyme. We hypothesize that binding of anionic substrates may promote similar structural changes. Further, the ability of the three catalytic chains in the trimer to access the open and closed active‐site conformations simultaneously suggests a cyclic catalytic mechanism, in which at least one of the chains is in an open conformation suitable for substrate binding whereas another chain is closed for catalytic turnover. Based on the many conformations observed for the chains in the isolated catalytic trimer to date, we propose that allosteric activation of the holoenzyme occurs by release of quaternary constraint into an ensemble of active‐site conformations.
Collaborative Planning in Process: An Ethnomethodological Perspective
Authors: Lee Josephine , Burch Alfred Rue 
Published: August 2017

Following Ellis's () call for more social and process‐oriented planning research, this study explores how learners approach collaborative planning tasks in the classroom as a locally contingent activity in situ. Drawing on ethnomethodology and conversation analysis, the present study focuses on a group planning stage that precedes the final task of delivering a presentation. Fine‐grained analyses of the interaction reveal that group planning is essentially a nonlinear, social, and pragmatic activity wherein the students manage participant roles, resolve disputes and misunderstandings, and collectively work toward effective task completion. These findings highlight that, although the groups begin with the same task‐as‐workplan (Breen, ; Seedhouse, ), the students’ concerns are driven by locally constructed goals and plans‐in‐process, and as they work toward a group consensus they are required to deal with a wide range of social and interactional contingencies.
The system capacity view of aging and longevity
Authors: Han Jing‐Dong J. , Hou Lei , Sun Na , Xu Chi , McDermott Joseph , Wang Dan 
Published: August 2017

BackgroundAging is a complex systems level problem that needs a systems level solution. However, system models of aging and longevity, although urgently needed, are still lacking, largely due to the paucity of conceptual frameworks for modeling such a complex process.ResultsWe propose that aging can be viewed as a decline in system capacity, defined as the maximum level of output that a system produces to fulfill demands. Classical aging hallmarks and anti‐aging strategies can be well‐aligned to system capacity. Genetic variants responsible for lifespan variation across individuals or species can also be explained by their roles in system capacity. We further propose promising directions to develop systems approaches to modulate system capacity and thus extend both healthspan and lifespan.ConclusionsThe system capacity model of aging provides an opportunity to examine aging at the systems level. This model predicts that the extent to which aging can be modulated is normally limited by the upper bound of the system capacity of a species. Within such a boundary, aging can be delayed by moderately increasing an individual’s system capacity. Beyond such a boundary, increasing the upper bound is required, which is not unrealistic given the unlimited potential of regenerative medicine in the future, but it requires increasing the capacity of the whole system instead of only part of it.
Models, methods and tools for ancestry inference and admixture analysis
Authors: Yuan Kai , Zhou Ying , Ni Xumin , Wang Yuchen , Liu Chang , Xu Shuhua 
Published: August 2017

BackgroundGenetic admixture refers to the process or consequence of interbreeding between two or more previously isolated populations within a species. Compared to many other evolutionary driving forces such as mutations, genetic drift, and natural selection, genetic admixture is a quick mechanism for shaping population genomic diversity. In particular, admixture results in “recombination” of genetic variants that have been fixed in different populations, which has many evolutionary and medical implications.ResultsHowever, it is challenging to accurately reconstruct population admixture history and to understand of population admixture dynamics. In this review, we provide an overview of models, methods, and tools for ancestry inference and admixture analysis.ConclusionsMany methods and tools used for admixture analysis were originally developed to analyze human data, but these methods can also be directly applied and/or slightly modified to study non‐human species as well.
How Do Psychological Risk Factors Predict Sexual Outcomes? A Comparison of Four Models of Young Women’s Sexual Outcomes
Authors: Tutino Jessica S. , Ouimet Allison J. , Shaughnessy Krystelle 
Published: August 2017

Abstract

Background
Recent research findings suggest that women who report high anxiety sensitivity (AS; the fear of physiologic sensations associated with anxiety) also report increased sexual dysfunction and decreased sexual satisfaction. Moreover, findings suggest that maladaptive emotion regulation (ER) can contribute to the relation between AS and psychological distress, thereby indirectly influencing sexual outcomes. Identifying relations among these variables and how they specifically relate to sexual outcomes could be vital for diagnostic and therapeutic purposes. As such, a comparison of different models of sexual outcomes that encompass psychological and sexual risk factors is needed.

Aim
To compare four psychological models of women’s sexual outcomes in a cross-sectional sample and specifically to investigate whether psychological factors (ie, AS, ER, psychological distress) uniquely or jointly predict related, but distinct, sexual outcomes in women: sexual functioning, sexual quality of life, and frequency of sexual activity.

Methods
Women (N = 316) completed an online survey that included the Anxiety Sensitivity Index–3, Difficulties with Emotion Regulation Scale, Depression Anxiety Stress Scales, Sexual Quality of Life Scale–Female, Female Sexual Function Index, and Sexual Experiences Questionnaire–Female.

Outcomes
Outcome variables included women’s self-reported sexual functioning, sexual quality of life, and frequency of sexual activity.

Results
Path analysis models demonstrated that psychological factors predicted orgasm, sexual pain, sexual quality of life, and frequency of partnered sexual activity in women but predicted sexual desire, arousal, lubrication, and frequency of solitary sexual activity to a lesser degree. We found that ER significantly accounted for the relation between AS and psychological distress through mediation and moderation pathways.

Clinical Translation
Clinicians would benefit from incorporating psychological risk factors in their assessment and interventions of women’s sexual concerns.

Strengths and Limitations
This is the first study to compare models of women’s sexual lives using indicators of mental and sexual health. However, our study was limited to a cross-sectional sample of young women in one university setting.

Conclusions
AS, ER, and psychological distress are related to sexual functioning, sexual quality of life, and frequency of partnered sexual activity in young women. Psychological risk factors should be taken into consideration to better understand women’s sexual lives.
Risk Factors for Erectile Dysfunction in Men with HTLV-1
Authors: de Oliveira Cassius José Vitor , Neto José Abraão Carneiro , Andrade Rosana C.P. , Rocha Paulo Novis , de Carvalho Filho Edgar Marcelino 
Published: August 2017

Abstract

Background
Erectile dysfunction (ED) occurs in more than 50% of patients with human T-cell lymphotropic virus type 1 (HTLV-1) infection. In the general population, atherosclerosis is the main risk factor related to ED.

Aim
To compare the contribution of neurologic disorders from HTLV-1 with that of atherosclerosis as risk factors for ED in men with HTLV-1.

Methods
In this cross-sectional study, men 18 to 70 years old with HTLV-1 were classified into one of two groups according to the presence or absence of ED. They were compared for obesity, waist circumference, dyslipidemia, metabolic syndrome, diabetes mellitus, high blood pressure, and neurologic manifestations. Comparisons between proportions were performed using the χ2 or Fisher exact test. Logistic regression analysis was performed to identify predictors of ED. Subjects with HTLV-1 were classified into three groups based on Osame's Disability Motor Scale and the Expanded Disability Status Scale: (i) HTLV-1 carriers; (ii) probable HTLV-1–associated myelopathy or tropical spastic paraparesis; and (iii) definitive HTLV-1–associated myelopathy or tropical spastic paraparesis. The International Index of Erectile Function was used to determine the degree of ED.

Results
In univariate logistic regression, age older 60 years (P = .003), diabetes mellitus (P = .042), and neurologic disease (P &lt; .001) were associated with ED. In the multivariate model, the odds of ED was highest in patients with neurologic disease (odds ratio = 22.1, 95% CI = 5.3–92.3), followed by high blood pressure (odds ratio = 6.3, 95% CI = 1.4-30.5) and age older than 60 years (odds ratio = 4.6, 95% CI = 1.3–17.3).

Clinical Implications
In men infected with HTLV-1, neurologic dysfunction is a stronger predictor of ED than risk factors for atherosclerosis.

Strengths and Limitations
The small number of patients limited the power of the statistical analysis, but clearly neurologic manifestations had a greater association with ED than risk factors for atherosclerosis, and there was no association between metabolic syndrome and severity of ED.

Conclusion
Neurologic impairment is the major cause of ED in individuals infected with HTLV-1 and risk factors for atherosclerosis did not have a strong relation with ED in this population.
Plasma Leptin and Reduced FEV1 and FVC in Chronic Spinal Cord Injury
Authors: Garshick Eric , Walia Palak , Goldstein Rebekah L. , Teylan Merilee , Lazzari Antonio A. , Tun Carlos G. , Hart Jaime E. 
Published: August 2017

AbstractBackgroundAdipose tissue produces leptin, which is pro‐inflammatory, and adiponectin, which has anti‐inflammatory properties. Participants with chronic spinal cord injury (SCI) have increased body fat and are at increased risk for respiratory illness.ObjectiveTo assess the associations between leptin and adiponectin with pulmonary function in a chronic SCI cohort.DesignCross‐sectional study.SettingVeterans Affairs Medical Center.ParticipantsA total of 285 participants (237 men and 48 women) with chronic SCI with mean (standard deviation) injury duration 17.8 (13.2) years from the VA Boston and the community participating in an epidemiologic study assessing factors associated with respiratory health.MethodsParticipants (24.6% cervical American Spinal Injury Association Impairment Scale (AIS) level A, B, and C; 33.6% other AIS A, B, and C; 41.8% AIS D) provided a blood sample, completed a respiratory health questionnaire, and underwent spirometry. Linear regression methods were used to assess cross‐sectional associations between plasma leptin and adiponectin with spirometric measures of pulmonary function adjusted for age, race, gender, and height. Level and severity of SCI, mobility mode, body mass index, smoking, chronic obstructive pulmonary disease, asthma, chest injury history, laboratory batch, and other potential confounders were also considered.Main Outcome Measurementsforced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), and FEV1/FVC.ResultsThere was a statistically significant inverse relationship between plasma leptin assessed in quartiles or as a continuous covariate with FEV1 and FVC. In fully adjusted models, each interquartile range (16,214 pg/mL) increase in leptin was associated with a significant decrease in FEV1 (−93.1 mL; 95% confidence interval = −166.2, −20.0) and decrease in FVC (−130.7 mL; 95% confidence interval = −219.4, −42.0). There were no significant associations between leptin and FEV1/FVC or between plasma adiponectin with FEV1, FVC, or FEV1/FVC.ConclusionPlasma leptin in individuals with chronic SCI is inversely associated with FEV1 and FVC, independently of SCI level and severity and other covariates. This finding suggests that plasma leptin may contribute to reduced pulmonary function in chronic SCI.Level of EvidenceII
Cross-linked decellularized porcine corneal graft for treating fungal keratitis
Authors: Lin Yongliang , Zheng Qinxiang , Hua Shanshan , Meng Yongchun , Chen Wei , Wang Yifei 
Published: August 2017

AbstractThis study aims to develop a cross-linked decellularized porcine corneal graft (cDPC) as a substitute for lamellar donor corneas and to evaluate the feasibility of using cDPC to treat fungal keratitis. The cDPC was prepared by decellularization, chemical crosslinking and γ-ray irradiation. Transparency, effectiveness of decellularization and biomechanical strength of cDPC were evaluated. The safety and efficacy of using cDPC to treat fungal keratitis were evaluated in the rabbit model. The transparency of cDPC was similar to that of a native porcine cornea (NPC), and no intact cells were observed in cDPC except for an insignificant amount of residual shrinking cellular nucleus. Compared to the NPC, the biomechanical strength of the cDPC was significantly increased. In the rabbit model of lamellar keratoplasty, the implanted cDPC reduced the incidence of corneal perforation, and also maintained transparency in majority. The results of this study suggest that the cDPC is capable of restoring the original transparency of cornea while effectively treating fungal keratitis. The cDPC is a highly promising ideal substitute for the donor human cornea.
Influences of ethanol on the structure of toxic trans-crotonaldehyde in mitochondria coming from rat myocardium
Authors: Su Yanbin , Ma Xiaowei , Su Yanwen , Mu Tongxing , Li Yanhe , Jiang Ning , Su Yuyun , Zhang Qi 
Published: August 2017

AbstractInappropriate use of ethanol (EtOH) had led to noticeable health problems, but a beneficial phenomenon was found that EtOH displayed unique influences for toxic trans-crotonaldehyde (TCA) derived from mitochondrial lipid peroxidation. The influences of EtOH on the structure of TCA were systematically probed by UV-vis & Raman spectroscopy in the absence and presence of mitochondria, respectively. The maximum UV-vis peak at 301 nm of TCA was red shifted by hydroxyl (-OH) and methyl (-CH3) of EtOH, respectively. Raman stretching band of aldehyde (-CH=O) of TCA (TCA-CH=O) was split by the -CH3 of EtOH. The -CH3 increased TCA-CH=O stretching frequency while the -OH induced it. The more exposed -OH, the less stretching frequency. The ectopic -CH3 red shifted the UV-vis peak at 301 nm and Raman band of TCA-CH=O. In mitochondria, EtOH red shifted Raman stretching band of TCA-CH=O. Raman stretching bands of C-H, C-O and C-C of EtOH were red shifted, while Raman stretching bands of -CH2 and C-C-O of EtOH disappeared. The paper unearths the influences of EtOH to trap and transform the structure of TCA-CH=O. This discovery has an important contribution to eliminate TCA in order to protect and repair mtDNA by means of the decrease of 8-oxoG.
ITGA1 is a pre-malignant biomarker that promotes therapy resistance and metastatic potential in pancreatic cancer
Authors: Gharibi Armen , La Kim Sa , Molnar Justin , Brambilla Daniel , Adamian Yvess , Hoover Malachia , Hong Julie , Lin Joy , Wolfenden Laurelin , Kelber Jonathan A. 
Published: August 2017

AbstractPancreatic ductal adenocarcinoma (PDAC) has single-digit 5-year survival rates at <7%. There is a dire need to improve pre-malignant detection methods and identify new therapeutic targets for abrogating PDAC progression. To this end, we mined our previously published pseudopodium-enriched (PDE) protein/phosphoprotein datasets to identify novel PDAC-specific biomarkers and/or therapeutic targets. We discovered that integrin alpha 1 (ITGA1) is frequently upregulated in pancreatic cancers and associated precursor lesions. Expression of ITGA1-specific collagens within the pancreatic cancer microenvironment significantly correlates with indicators of poor patient prognosis, and depleting ITGA1 from PDAC cells revealed that it is required for collagen-induced tumorigenic potential. Notably, collagen/ITGA1 signaling promotes the survival of ALDH1-positive stem-like cells and cooperates with TGFβ to drive gemcitabine resistance. Finally, we report that ITGA1 is required for TGFβ/collagen-induced EMT and metastasis. Our data suggest that ITGA1 is a new diagnostic biomarker and target that can be leveraged to improve patient outcomes.
Switching transients in a 2 × 15 kV 16.7 Hz autotransformer railway system
Authors: Chmielewski Tomasz , Oramus Piotr , Koska Krzysztof 
Published: August 2017

This study presents the analysis of transient states generated along the traction catenary during switching operation in the main supply substation unit. For this purpose, a Swedish autotransformer railway system operating at 15 kV and 16.7 Hz has been chosen as a reference. The simulations of abovementioned system were conducted using EMTP‐ATP software. This study presents results of simulations for various conditions and at different loads. The main outcome of the analysis is determination of transient currents and voltages in the system during catenary energisation and de‐energisation process. Due to the presence of saturable autotransformers along the catenary the flow of excessive inrush current may lead not only to the overloading and as a consequence main breaker tripping but may also cause slow‐front overvoltages. In order to represent the worst case conditions parametric study was performed. It includes variable tripping time of the main circuit breaker and pre‐existing residual core flux. The results of the analysis show that the system response is strongly dependent on the breaker closing and opening times. As a consequence, it is possible to determine safe switching conditions in order to avoid large overvoltages or accidental tripping.
Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples
Authors: Arulandhu Alfred J. , Staats Martijn , Hagelaar Rico , Voorhuijzen Marleen M. , Prins Theo W. , Scholtens Ingrid , Costessi Adalberto , Duijsings Danny , Rechenmann François , Gaspar Frédéric B. , Barreto Crespo Maria Teresa , Holst-Jensen Arne , Birck Matthew , Burns Malcolm , Haynes Edward , Hochegger Rupert , Klingl Alexander , Lundberg Lisa , Natale Chiara , Niekamp Hauke , Perri Elena , Barbante Alessandra , Rosec Jean-Philippe , Seyfarth Ralf , Sovová Tereza , Van Moorleghem Christoff , van Ruth Saskia , Peelen Tamara , Kok Esther 
Published: August 2017

Abstract
DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.
Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity
Authors: Lee Yongchan , Nishizawa Tomohiro , Takemoto Mizuki , Kumazaki Kaoru , Yamashita Keitaro , Hirata Kunio , Minoda Ayumi , Nagatoishi Satoru , Tsumoto Kouhei , Ishitani Ryuichiro , Nureki Osamu 
Published: August 2017

AbstractThe triose-phosphate/phosphate translocator (TPT) catalyzes the strict 1:1 exchange of triose phosphate, 3-phosphoglycerate and inorganic phosphate across the chloroplast envelope, and plays crucial roles in photosynthesis. Despite rigorous studies for more than 40 years, the molecular mechanism of TPT is poorly understood due to the lack of structural information. Here we report crystal structures of TPT bound to two different substrates, 3-phosphoglycerate and inorganic phosphate, in occluded conformations. The structures reveal that TPT adopts a 10-transmembrane drug/metabolite transporter fold. Both substrates are bound within the same central pocket, where conserved lysine, arginine, and tyrosine residues recognize the shared phosphate group. A structural comparison with the outward-open conformation of the bacterial drug/metabolite transporter suggests a rocking-type motion of helix bundles, and molecular dynamics simulations support a model in which this helix rocking is tightly coupled to the substrate binding, to ensure strict 1:1 exchange. These results reveal the unique mechanism of sugar phosphate/phosphate exchange by TPT.