bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short-Term and Working Memory Treatments for Improving Sentence Comprehension in Aphasia: A Review and a Replication Study
Authors: Salis Christos , Hwang Faustina , Howard David , Lallini Nicole 
Published: February 2017

AbstractAlthough the roles of verbal short-term and working memory on spoken sentence comprehension skills in persons with aphasia have been debated for many years, the development of treatments to mitigate verbal short-term and working memory deficits as a way of improving spoken sentence comprehension is a new avenue in treatment research. In this article, we review and critically appraise this emerging evidence base. We also present new data from five persons with aphasia of a replication of a previously reported treatment that had resulted in some improvement of spoken sentence comprehension in a person with aphasia. The replicated treatment did not result in improvements in sentence comprehension. We forward recommendations for future research in this, admittedly weak at present, but important clinical research avenue that would help improve our understanding of the mechanisms of improvement of short-term and working memory training in relation to sentence comprehension.
Sulfide-responsive transcriptional repressor SqrR functions as a master regulator of sulfide-dependent photosynthesis
Authors: Shimizu Takayuki , Shen Jiangchuan , Fang Mingxu , Zhang Yixiang , Hori Koichi , Trinidad Jonathan C. , Bauer Carl E. , Giedroc David P. , Masuda Shinji 
Published: February 2017

Significance
Hydrogen sulfide is a universal bioactive molecule that functions in both prokaryotes and eukaryotes. However, little is known about intra- and extracellular sulfide-sensing mechanisms. Here we show that the sulfide-regulated repressor SqrR from a purple bacterium forms an intramolecular tetrasulfide bond in response to sulfide stress in vivo and organic persulfides in vitro, revealing the importance of this cysteine modification for sulfide sensing in cells. These findings provide new insights into bacterial sulfide homeostasis and its potential applications in synthetic biology. Given that purple bacteria retain characteristics of ancestral photosynthesis and photosynthetic electron transfer, the functional characterization of SqrR also provides new information on plausible mechanisms that regulated electron flow early in the evolution of photosynthesis.
Brownian motion of solitons in a Bose–Einstein condensate
Authors: Aycock Lauren M. , Hurst Hilary M. , Efimkin Dmitry K. , Genkina Dina , Lu Hsin-I , Galitski Victor M. , Spielman I. B. 
Published: February 2017

Significance
Solitons, spatially localized, mobile excitations resulting from an interplay between nonlinearity and dispersion, are ubiquitous in physical systems from water channels and oceans to optical fibers and Bose–Einstein condensates (BECs). From our pulse throbbing at our wrists to rapidly moving tsunamis, solitons appear naturally at a wide range of scales. In nonlinear optical fibers, solitons can travel long distances with applications for communication technology and potential for use in quantum switches and logic. Understanding how random processes contribute to the decay and the diffusion of solitons is essential to advancing these technologies.
Extending enzyme molecular recognition with an expanded amino acid alphabet
Authors: Windle Claire L. , Simmons Katie J. , Ault James R. , Trinh Chi H. , Nelson Adam , Pearson Arwen R. , Berry Alan 
Published: February 2017

Significance
The remarkable power of enzymes as catalysts is derived from the precise spatial positioning of amino acids as a result of a polypeptide folding into its native, active fold. Protein engineers have a wide arsenal of tools available to alter the properties of enzymes but, until recently, have been limited to replacement of amino acids with one of the other naturally occurring proteogenic amino acids. Here we describe a protein engineering approach to introduce a noncanonical amino acid that results in altered substrate specificity of an aldolase to produce a novel activity that cannot be achieved by simple substitution with any of the canonical amino acids.
Modeling the two-way feedback between contractility and matrix realignment reveals a nonlinear mode of cancer cell invasion
Authors: Ahmadzadeh Hossein , Webster Marie R. , Behera Reeti , Jimenez Valencia Angela M. , Wirtz Denis , Weeraratna Ashani T. , Shenoy Vivek B. 
Published: February 2017

Significance
The mechanical cross talk between intracellular and extracellular forces can promote the invasive potential of tumor cells in tumors. Using a quantitative model, we elucidate the two-way feedback loop between stress-dependent cell contractility and matrix fiber realignment and strain stiffening, which enables the cells to polarize and enhance their contractility to break free from the tumor and invade into the matrix. Our model predicts that intermediate matrix stiffness is optimal for invasion, and we find a positive correlation between cell elongation and alignment of fibers in the matrix. Importantly, our model can be used to explain how morphological and structural changes in the tumor microenvironment, such as elevated rigidity and fiber alignment prior to cell invasion, are prognostic of the malignant phenotype.
Spontaneous activity in the piriform cortex extends the dynamic range of cortical odor coding
Authors: Tantirigama Malinda L. S. , Huang Helena H.-Y. , Bekkers John M. 
Published: February 2017

Significance
Sensory neurons are often spontaneously active even in the absence of the relevant stimuli, raising the question, Is this background activity a bug or a feature of neural circuits? Using in vivo calcium imaging in mice, we show that neurons in the primary olfactory (piriform) cortex are spontaneously active when the animal is breathing unodorized air and this activity is entirely driven by spontaneous firing in the upstream olfactory bulb. When the animal smells an odor, some piriform neurons fire more strongly, and others have their spontaneous activity suppressed. By allowing two-way changes in firing, spontaneous background activity serves as a mechanism to extend the range of odor coding.
AgRP to Kiss1 neuron signaling links nutritional state and fertility
Authors: Padilla Stephanie L. , Qiu Jian , Nestor Casey C , Zhang Chunguang , Smith Arik W. , Whiddon Benjamin B. , Rønnekleiv Oline K. , Kelly Martin J. , Palmiter Richard D. 
Published: February 2017

Significance
Women suffering from malnutrition and athletes with low body fat become infertile as a result of low gonadotropin secretion. Gonadotropin release is determined by a neural endocrine circuit; however, the metabolic cues that are responsible for attenuating this axis during starvation remain unclear. Here, we find that starvation-activated agouti-related peptide (AgRP) neurons can inhibit the reproductive neuroendocrine circuit. Furthermore, artificial activation of genetically defined AgRP neurons is sufficient to delay estrous cycle length and parturition in female mice. This work demonstrates a mechanism by which AgRP neurons can relay metabolic information to the fertility axis during starvation.
Ontology of Fake: Discerning the Philippine Elite
Authors: Reyes Angela 
Published: February 2017

AbstractHilary Putnam (1975) proposes that a “natural kind” term relies on a division of linguistic labor in which experts discern what is or is not a member of a kind. Centering on a Philippine-elite social kind term, this essay examines how self-appointed experts develop and share “scientific” instruments, or tests, that discern whether someone is a “real” or “fake” elite. These tests report about signs of realness and fakeness by assigning “gentle” and “rough” qualities to speech and body of differentiated social types. This essay demonstrates that such qualia are central to shaping ontologies of social types; that the discerning subject, who speaks from an elevated social position as reflexive expert, is critical to this process; and that the discerner shares expertise by developing tests that rest on different ontologies of emblem. The essay argues that discerning Philippine elite types and their aspiring subtypes and countertypes presupposes an overarching ontology of fake that already renders real elites as fakes.
Final report on APMP supplementary comparison of industrial platinum resistance thermometer for range -50 °C to 400 °C. (APMP.T-S6)
Authors: Ali Nurulaini Md , Othman Hafidzah , Ho Mong-Kim , Yang Inseok , Gabi Victor , Zhang Zhe , Sheng Ying , Hu Jing , Zhang Jintao , Tsai Shu-Fei , Liao Su-Chuion , Alam Md Shafiqul , Norranim Uthai , Yaokulbodee Charuayrat , Liedberg Hans , Ahmed Mohamed Gamal , Harba Naser , Flaifel Mustafa Fuad , Suherlan  , Achmadi Aditya , Haoyuan Kho , Yan Fan , Kwee Neoh Boon , Binh Pham Thanh , Ragay Monalisa 
Published: February 2017

The National Metrology Laboratory, Malaysia (NML-SIRIM) had coordinated the Supplementary Comparison of Industrial Platinum Resistance Thermometer (IPRT) started from July 2009 until April 2011 together with the National Measurement Institute of Australia (NMIA) and Korea Research Institute of Standards and Science (KRISS). This comparison was opened to all APMP members and 16 participants had taken part in order to consolidate or improve their calibration and measurement capabilities (CMCs). Three units of artefacts 100-ohm IPRT belonging to NML-SIRIM, NMIA and KRISS were used and three loops of measurement were run in parallel to shorten the circulation time. The stability of artefacts was monitored with initial and final ice point measurement by each laboratory. The participants need to perform measurement at temperature points (0,-50,-30, 0, 100, 200, 300, 400,0) °C. All submitted data were compiled and adjusted at nominal temperature and by using the linkage from NMIA and KRISS as reference value for all three loops , the temperature deviation from participants from different loops can be compared. The approach of Birge Ratio for final exclusion comprised all the excluded results from the analysis of each loop and the measurement performance for each participant were summarized by the En number value.
Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Final report, on-going key comparison BIPM.QM-K1, ozone at ambient level, comparison with NIST, July 2015
Authors: Viallon Joële , Moussay Philippe , Wielgosz Robert , Hodges Joe , Norris James E 
Published: February 2017

As part of the ongoing key comparison BIPM.QM-K1, a comparison has been performed between the ozone national standard of the National Institute of Standards and Technology (NIST) and the common reference standard of the key comparison, maintained by the Bureau International des Poids et Mesures (BIPM). The instruments have been compared over a nominal ozone amount-of-substance fraction range of 0 nmol/mol to 500 nmol/mol.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Frobenius reciprocity and the Haagerup tensor product
Authors: Crisp Tyrone 
Published: February 2017

In the context of operator-space modules over

C
∗

C^*

-algebras, we give a complete characterisation of those

C
∗

C^*

-correspondences whose associated Haagerup tensor product functors admit left adjoints. The characterisation, which builds on previous joint work with N. Higson, exhibits a close connection between the notions of adjoint operators and adjoint functors. As an application, we prove a Frobenius reciprocity theorem for representations of locally compact groups on operator spaces: the functor of unitary induction for a closed subgroup

H
H

of a locally compact group

G
G

admits a left adjoint in this setting if and only if

H
H

is cocompact in

G
G

. The adjoint functor is given by the Haagerup tensor product with the operator-theoretic adjoint of Rieffel’s induction bimodule.
Diagnostic Testing Approaches for Activated Protein C Resistance and Factor V Leiden
Authors: Perez Botero Juliana , Majerus Julie A. , Strege Ann K. , Johnson Ryan D. , Chen Dong , Pruthi Rajiv K. 
Published: February 2017

AbstractObjectivesTo analyze the economic impact of testing for activated protein C resistance (APC-R) due to factor V Leiden (FVL) mutation with APC-R with reflexive FVL genotyping (algorithmic approach) or genotyping alone.MethodsOptumLabs Data Warehouse (OLDW) data were used to assess testing approaches. Insurance claims for APC-R and FVL in 2013 were compared with the Mayo Clinic database. Centers for Medicare & Medicaid Services diagnostic fee schedules were used to assign costs.ResultsOf 19.3 million OLDW-covered individuals, 74,242 (0.385%) received 75,608 tests: APC-R, 2,265 (2.9%); FVL genotyping, 70,619 (90.1%); and both APC-R and FVL, 2,724 (7.0%). In total, 1,317 tests were performed at Mayo Clinic: APC-R with reflex FVL (1,256; 95.4%) and FVL alone (61; 4.6%). Costs per evaluated individual and per total population (person/year) in OLDW and algorithmic approach were $83.77 vs $36.38 and $0.32 vs $0.14, respectively.ConclusionsThe cost-optimized algorithmic approach reduces health care costs.
Resequencing Study Identifies Rare Renin–Angiotensin–Aldosterone System Variants Associated With Blood Pressure Salt-Sensitivity: The GenSalt Study
Authors: Kelly Tanika N. , Li Changwei , Hixson James E. , Gu Dongfeng , Rao Dabeeru C. , Huang Jianfeng , Rice Treva K. , Chen Jichun , Cao Jie , Li Jianxin , Anderson Christopher E. , He Jiang 
Published: February 2017

Abstract

BACKGROUND
The role of rare variants in blood pressure (BP) salt-sensitivity is unknown. We conducted a resequencing study of the renin–angiotensin–aldosterone system (RAAS) to identify rare variants associated with BP salt-sensitivity among participants of the Genetic Epidemiology Network of Salt-Sensitivity (GenSalt) study.

METHODS
The GenSalt study was conducted among 1,906 participants who underwent a 7-day low-sodium (51.3 mmol sodium/day) followed by a 7-day high-sodium feeding study (307.8 mmol sodium/day). The 300 most salt-sensitive and 300 most salt-resistant GenSalt participants were selected for the resequencing study. Seven RAAS genes were resequenced using capillary-based sequencing methods. Rare variants were tested for association with BP salt-sensitivity using traditional burden tests. Single-marker analyses were employed to test associations of low-frequency and common variants.

RESULTS
Aggregate rare variant analysis revealed an association of the RAAS pathway with BP salt-sensitivity. Carriers of rare RAAS variants had a 1.55-fold [95% confidence interval (CI): 1.15, 2.10] higher odds of salt-sensitivity compared to noncarriers (P = 0.004), a finding which was significant after Bonferroni correction. A nominal association of the APLN gene with salt-sensitivity was also identified, with rare APLN variants conferring a 2.22-fold (95% CI: 1.05, 6.58) higher odds of salt-sensitivity (P = 0.03). Single-marker analyses did not identify variant-BP salt-sensitivity associations after Bonferroni adjustment. A nominal association of a low-frequency, missense RENBP variant was identified. Each minor allele of rs78377269 conferred a 2.21-fold (95% CI: 1.10, 4.42) increased odds of salt-sensitivity (P = 0.03).

CONCLUSIONS
This study presents of the first evidence of a contribution of rare RAAS variants to BP salt-sensitivity.
Clinical Trial RegistryTrial Number: NCT00721721
Changes associated with Ebola virus adaptation to novel species
Authors: Pappalardo Morena , Reddin Ian G , Cantoni Diego , Rossman Jeremy S , Michaelis Martin , Wass Mark N 
Published: February 2017

Abstract

Motivation
Ebola viruses are not pathogenic but can be adapted to replicate and cause disease in rodents. Here, we used a structural bioinformatics approach to analyze the mutations associated with Ebola virus adaptation to rodents to elucidate the determinants of host-specific Ebola virus pathogenicity.

Results
We identified 33 different mutations associated with Ebola virus adaptation to rodents in the proteins GP, NP, L, VP24 and VP35. Only VP24, GP and NP were consistently found mutated in rodent-adapted Ebola virus strains. Fewer than five mutations in these genes seem to be required for the adaptation of Ebola viruses to a new species. The role of mutations in GP and NP is not clear. However, three VP24 mutations located in the protein interface with karyopherin α5 may enable VP24 to inhibit karyopherins and subsequently the host interferon response. Three further VP24 mutations change hydrogen bonding or cause conformational changes. Hence, there is evidence that few mutations including crucial mutations in VP24 enable Ebola virus adaptation to new hosts. Since Reston virus, the only non-human pathogenic Ebolavirus species circulates in pigs in Asia, this raises concerns that few mutations may result in novel human pathogenic Ebolaviruses.

Supplementary information
Supplementary data are available at Bioinformatics online.
nala: text mining natural language mutation mentions
Authors: Cejuela Juan Miguel , Bojchevski Aleksandar , Uhlig Carsten , Bekmukhametov Rustem , Kumar Karn Sanjeev , Mahmuti Shpend , Baghudana Ashish , Dubey Ankit , Satagopam Venkata P , Rost Burkhard 
Published: February 2017

Abstract

Motivation
The extraction of sequence variants from the literature remains an important task. Existing methods primarily target standard (ST) mutation mentions (e.g. ‘E6V’), leaving relevant mentions natural language (NL) largely untapped (e.g. ‘glutamic acid was substituted by valine at residue 6’).

Results
We introduced three new corpora suggesting named-entity recognition (NER) to be more challenging than anticipated: 28–77% of all articles contained mentions only available in NL. Our new method nala captured NL and ST by combining conditional random fields with word embedding features learned unsupervised from the entire PubMed. In our hands, nala substantially outperformed the state-of-the-art. For instance, we compared all unique mentions in new discoveries correctly detected by any of three methods (SETH, tmVar, or nala). Neither SETH nor tmVar discovered anything missed by nala, while nala uniquely tagged 33% mentions. For NL mentions the corresponding value shot up to 100% nala-only.

Availability and Implementation
Source code, API and corpora freely available at: http://tagtog.net/-corpora/IDP4+.

Supplementary information
Supplementary data are available at Bioinformatics online.
MapReduce for accurate error correction of next-generation sequencing data
Authors: Zhao Liang , Chen Qingfeng , Li Wencui , Jiang Peng , Wong Limsoon , Li Jinyan 
Published: February 2017

Abstract

Motivation
Next-generation sequencing platforms have produced huge amounts of sequence data. This is revolutionizing every aspect of genetic and genomic research. However, these sequence datasets contain quite a number of machine-induced errors—e.g. errors due to substitution can be as high as 2.5%. Existing error-correction methods are still far from perfect. In fact, more errors are sometimes introduced than correct corrections, especially by the prevalent k-mer based methods. The existing methods have also made limited exploitation of on-demand cloud computing.

Results
We introduce an error-correction method named MEC, which uses a two-layered MapReduce technique to achieve high correction performance. In the first layer, all the input sequences are mapped to groups to identify candidate erroneous bases in parallel. In the second layer, the erroneous bases at the same position are linked together from all the groups for making statistically reliable corrections. Experiments on real and simulated datasets show that our method outperforms existing methods remarkably. Its per-position error rate is consistently the lowest, and the correction gain is always the highest.

Availability and Implementation
The source code is available at bioinformatics.gxu.edu.cn/ngs/mec.

Supplementary information
Supplementary data are available at Bioinformatics online.
An approach to infer putative disease-specific mechanisms using neighboring gene networks
Authors: Ansari Sahar , Donato Michele , Saberian Nafiseh , Draghici Sorin 
Published: February 2017

Abstract

Motivation
The ultimate goal of any experiment is to understand the biological phenomena underlying the condition investigated. This process often results in genes network through which a certain biological mechanism is explained. Such networks have been proven to be extremely useful, for the prediction of mechanisms of action of drugs or the responses of an organism to a specific impact (e.g. a disease, a treatment, etc.). Here, we introduce an approach able to build a network that captures the putative mechanisms at play in the given condition, by using datasets from multiple experiments studying the same phenotype. This method takes advantage of known interactions extracted from multiple sources such as protein–protein interactions and curated biological pathways. Based on such prior knowledge, we overcome the drawbacks of snap-shot data by considering the possible effects of each gene on its neighbors.

Results
We show the effectiveness of this approach in three different case studies and validate the results in two ways considering the identified genes and interactions between them. We compare our findings with the results of two widely-used methods in the same category as well as the classical approach of selecting differentially expressed (DE) genes in an investigated condition. The results show that ‘neighbor-net’ analysis is able to report biological mechanisms that are significantly relevant to the given diseases in all the three case studies, and performs better compared to all reference methods using both validation approaches.

Availability and Implementation
The proposed method is implemented as in R and will be available an a Bioconductor package.

Supplementary information
Supplementary data are available at Bioinformatics online.
Efficient inference for genetic association studies with multiple outcomes
Authors: Ruffieux Helene , Davison Anthony C. , Hager Jorg , Irincheeva Irina 
Published: February 2017

SUMMARY
Combined inference for heterogeneous high-dimensional data is critical in modern biology, where clinical and various kinds of molecular data may be available from a single study. Classical genetic association studies regress a single clinical outcome on many genetic variants one by one, but there is an increasing demand for joint analysis of many molecular outcomes and genetic variants in order to unravel functional interactions. Unfortunately, most existing approaches to joint modeling are either too simplistic to be powerful or are impracticable for computational reasons. Inspired by Richardson and others (2010, Bayesian Statistics 9), we consider a sparse multivariate regression model that allows simultaneous selection of predictors and associated responses. As Markov chain Monte Carlo (MCMC) inference on such models can be prohibitively slow when the number of genetic variants exceeds a few thousand, we propose a variational inference approach which produces posterior information very close to that of MCMC inference, at a much reduced computational cost. Extensive numerical experiments show that our approach outperforms popular variable selection methods and tailored Bayesian procedures, dealing within hours with problems involving hundreds of thousands of genetic variants and tens to hundreds of clinical or molecular outcomes.