bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term Survival After Surgery Compared With Concurrent Chemoradiation for Node-negative Small Cell Lung Cancer
Authors: Yang Chi-Fu Jeffrey , Chan Derek Y. , Shah Shivani A. , Yerokun Babatunde A. , Wang Xiaofei F. , D’Amico Thomas A. , Berry Mark F. , Jr David H. Harpole 
Published: May 2017

Objective:
To determine whether surgery with adjuvant chemotherapy offers a survival advantage over concurrent chemoradiation for patients with cT1-2N0M0 small cell lung cancer (SCLC).

Background:
Although surgery with adjuvant chemotherapy is the recommended treatment for patients with cT1-2N0M0 SCLC per international guidelines, there have been no prospective or retrospective studies evaluating the impact of surgery versus optimal medical management for cT1-2N0M0 SCLC.

Methods:
Outcomes of patients with cT1-2N0M0 SCLC who underwent surgery with adjuvant chemotherapy or concurrent chemoradiation in the National Cancer Data Base (2003–2011) were evaluated using Cox proportional hazards analyses and propensity-score-matched analyses.

Results:
During the study period, 681 (30%) patients underwent surgery with adjuvant chemotherapy and 1620 (70%) underwent concurrent chemoradiation. After propensity-score matching, all 14 covariates were well balanced between the surgery (n = 501) and concurrent chemoradiation (n = 501) groups. Surgery was associated with a higher overall survival (OS) than concurrent chemoradiation (5-year OS 47.6% vs 29.8%, P < 0.01). To minimize selection bias due to comorbidities, we limited the propensity-matched analysis to 492 patients with no comorbidities; surgery remained associated with a higher OS than concurrent chemoradiation (5-year OS 49.2% vs 32.5%, P < 0.01).

Conclusions:
In a national analysis, surgery with adjuvant chemotherapy was used in the minority of patients for early stage SCLC. Surgery with adjuvant chemotherapy for node-negative SCLC was associated with improved long-term survival when compared to concurrent chemoradiation. These results suggest a significant underuse of surgery among patients with early stage SCLC and support an increased role of surgery in multimodality therapy for cT1-2N0M0 SCLC.
Diagnostic, Infection Timing and Incidence Surveillance Applications of High Dynamic Range Chemiluminescent HIV Immuno-Assay Platforms
Authors: Grebe Eduard , Welte Alex , Hall Jake , Keating Sheila M. , Facente Shelley N. , Marson Kara , Martin Jeffrey N. , Little Susan J. , Price Matthew A. , Kallas Esper G. , Busch Michael P. , Pilcher Christopher D. , Murphy Gary ,   on behalf of the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA)
Published: May 2017

AbstractBackgroundCustom staging assays, including the Sedia HIV-1 Limiting Antigen Avidity EIA (LAg) and avidity modifications of the Ortho VITROS anti-HIV-1+2 and Abbott ARCHITECT HIV Ag/Ab Combo assays, are used to identify ‘recent’ infections in clinical settings and for cross-sectional HIV incidence estimation. However, the high dynamic range of chemiluminescent platforms allows differentiating recent and longstanding infection on signal intensity, and this raises the prospect of using unmodified diagnostic assays for infection timing and surveillance applications.MethodsWe tested a panel of 2,500 well-characterised specimens with estimable duration of HIV infection with the three assays and the unmodified ARCHITECT. Regression models were used to estimate mean durations of recent infection (MDRI), context-specific false-recent rates (FRR) and correlation between signal intensity and LAg measurements. A hypothetical epidemiological scenario was constructed to evaluate utility in surveillance applications.ResultsOver a range of MDRIs (reflecting recency discrimination thresholds), a diluted ARCHITECT-based RITA produced lower FRRs than the VITROS platform (FRR ≈ 0.5% and 1.5% respectively at MDRI of 200 days) and the unmodified diagnostic ARCHITECT produces incidence estimates with comparable precision to LAg (RSE ≈ 17.5% and 15% respectively at MDRI of 200 days). ARCHITECT S/CO measurements were highly correlated with LAg ODn measurements (r = 0.80) and values below 200 are strongly predictive of LAg recency and duration of infection less than one year.ConclusionsLow quantitative measurements from the unmodified ARCHITECT obviate the need for additional recency testing and its use is feasible in clinical staging and incidence surveillance applications.
Testing an alternative explanation for relatively greater base-sharing between Neanderthals and non-African humans
Authors: Amos William 
Published: May 2017

AbstractMost accept that non-African humans share ∼2% of their genome with Neanderthals (1) and that inter-breeding occurred between several archaic lineages (2-4). However, most evidence assumes that mutation rate is constant. It has been suggested that heterozygosity is mutagenic (5-8). If so, an alternative explanation of the data becomes possible. Instead of non-Africans sharing relatively more bases with Neanderthals due to interbreeding, Africans could appear unexpectedly divergent due to their mutation rate not having been lowered when diversity was lost during the out of Africa bottleneck. I therefore tested a series of predictions aimed at distinguishing mutation slowdown from inter-breeding. Predictions from mutation slowdown are generally better supported. For example, the signal used to infer inter-breeding remains even when Neanderthal sequences are excluded. I conclude that, while some inter-breeding probably did occur, an appreciable component of the signal seems better explained by mutation slowdown.
Experimental evidence that thermal selection shapes mitochondrial genome evolution
Authors: Lajbner Zdeněk , Pnini Reuven , Camus M. Florencia , Miller Jonathan , Dowling Damian K. 
Published: May 2017

AbstractMitochondria are essential organelles, found within eukaryotic cells, which contain their own DNA. Mitochondrial DNA (mtDNA) has traditionally been used in population genetic and biogeographic studies as a maternally-inherited and evolutionary-neutral genetic marker. However, it is now clear that polymorphisms within the mtDNA sequence are routinely non-neutral, and furthermore several studies have suggested that such mtDNA polymorphisms are also sensitive to thermal selection. These observations led to the formulation of the “mitochondrial climatic adaptation” hypothesis, for which all published evidence to date is correlational. Here, we use laboratory-based experimental evolution in the fruit fly,Drosophila melanogaster,to test whether thermal selection can shift population frequencies of two mtDNA haplogroups whose natural frequencies exhibit clinal associations with latitude along the Australian east-coast. We present experimental evidence that the thermal regime in which the laboratory populations were maintained, drove changes in haplogroup frequencies across generations. Our results strengthen the emerging view that intra-specific mtDNA variants are sensitive to selection, and suggest spatial distributions of mtDNA variants in natural populations of metazoans might reflect adaptation to climatic environments rather than within-population coalescence and diffusion of selectively-neutral haplotypes across populations.Impact SummaryWe applied experimental laboratory evolution to provide the first direct test of the “mitochondrial climatic hypothesis,” which predicts that the variation of mitochondrial genomes across natural distributions of metazoans can be shaped by thermal selection. Our design is the first of its kind when it comes to inferring the role of thermal selection in shaping mtDNA frequencies in nature. We harness two naturally occurring mtDNA haplotypes ofDrosophila melanogasterthat segregate along the east coast of Australia. One of these haplotypes predominates at sub-tropical northern latitudes and the other in the temperate and cooler south of the country. We then compete these haplotypes against each other in replicated experimental fly populations submitted to one of four different thermal regimes, in either the presence or absence of infection byWolbachia, a coevolved endosymbiont that also exhibits maternal transmission.We confirm that when evolving in the laboratory under warmer conditions, a haplotype naturally predominating in subtropical conditions outcompetes a haplotype that predominates at cooler Australian latitudes in the wild. We see this effect on haplotype frequencies in females in populations where latentWolbachiainfections had been purged.Our results also suggest that sex-specificity of mtDNA effects, and co-occurrence of other maternally-inherited microbiotic entities - of whichWolbachiais just one example - are likely to shape the trajectories of mitochondrial genome evolution in the wild.
Stimulus dependent diversity and stereotypy in the output of an olfactory functional unit
Authors: Arneodo Ezequiel M. , Penikis Kristina B. , Rabinowitz Neil , Cichy Annika , Zhang Jingji , Bozza Thomas , Rinberg Dmitry 
Published: May 2017

AbstractOlfactory inputs are organized in an array of parallel functional units (glomeruli), each relaying information from sensory neurons that express a given odorant receptor to a small population of output neurons, mitral/tufted (MT) cells. MT cells have complex temporal responses to odorants, but how these diverse responses relate to stimulus features is not known. We recorded in awake mice responses from “sister” MT cells that receive input from a functionally-characterized, genetically identified glomerulus, corresponding to a specific receptor (M72). Despite receiving similar inputs, sister MT cells exhibited temporally diverse, concentration variant, excitatory and inhibitory responses to most M72 ligands. In contrast, the strongest known ligand for M72 elicited temporally-stereotyped, early excitatory responses in all sister MT cells that persisted across all odor concentrations. Our data demonstrate that information about ligand affinity is encoded in the collective stereotypy or diversity of activity among sister MT cells within a glomerular functional unit in concentration-independent manner.
In-silico read normalization using set multi-cover optimization
Authors: Durai Dilip A , Schulz Marcel H 
Published: May 2017

AbstractDeBruijn graphs are a common assembly data structure for large sequencing datasets. But with the advances in sequencing technologies, assembling high coverage datasets has become a computational challenge. Read normalization, which removes redundancy in large datasets, is widely applied to reduce resource requirements. Current normalization algorithms, though efficient, provide no guarantee to preserve importantk-mers that form connections between regions in the graph. Here, normalization is phrased as aset multi-cover problemon reads and a heuristic algorithm, ORNA, is proposed. ORNA normalizes to the minimum number of reads required to retain allk-mers and their relativekmer abundances from the original dataset. Hence, all connections and coverage information from the original graph are preserved. ORNA was tested on various RNA-seq datasets with different coverage values. It was compared to the current normalization algorithms and was found to be performing better. It is shown that combining read error correction and normalization allows more accurate and resource efficient RNA assemblies compared to the original dataset. Further, an application was proposed in which multiple datasets were combined and normalized to predict novel transcripts that would have been missed otherwise. Finally, ORNA is a general purpose normalization algorithm that is fast and significantly reduces datasets with little loss of assembly quality.ORNA can be found underhttps://github.com/SchulzLab/ORNA
Self-organisation and positioning of bacterial protein clusters
Authors: Murray Seán M. , Sourjik Victor 
Published: May 2017

AbstractMany cellular processes require sub-cellular positioning of proteins. This can be due to passive mechanisms such as recruitment by existing landmarks or curvature sensing. However, in bacteria active self-positioning is likely to play a role in multiple processes, including the positioning of the future division site and cytoplasmic protein clusters. How can such dynamic clusters be formed and positioned? Here, we present a model for the self-organization and positioning of dynamic protein clusters into regularly repeating patterns based on a phase-locked Turing pattern. A single peak in the concentration is always positioned at mid-domain (mid-cell) while two peaks are positioned one at each quarter-position etc. Furthermore, domain growth results in peak-splitting and pattern doubling. We argue that the model may explain the regular positioning of the highly conserved Structural Maintenance of Chromosomes (SMC) complexes on the bacterial nucleoid and provides an attractive mechanism for the self-positioning of dynamic protein clusters in other systems.
Activations of Deep Convolutional Neural Network are Aligned with Gamma Band Activity of Human Visual Cortex
Authors: Kuzovkin Ilya , Vicente Raul , Petton Mathilde , Lachaux Jean-Philippe , Baciu Monica , Kahane Philippe , Rheims Sylvain , Vidal Juan R. , Aru Jaan 
Published: May 2017

Previous work demonstrated a direct correspondence between the hierarchy of the human visual areas and layers of deep convolutional neural networks (DCNN) trained on visual object recognition. We used DCNNs to investigate which frequency bands correlate with feature transformations of increasing complexity along the ventral visual pathway. By capitalizing on intracranial depth recordings from 100 patients and 11293 electrodes we assessed the alignment between the DCNN and signals at different frequency bands in different time windows. We found that gamma activity, especially in the low gamma-band (30 – 70 Hz), matched the increasing complexity of visual feature representations in the DCNN. These findings show that the activity of the DCNN captures the essential characteristics of biological object recognition not only in space and time, but also in the frequency domain. These results also demonstrate the potential that modern artificial intelligence algorithms have in advancing our understanding of the brain.Significance StatementRecent advances in the field of artificial intelligence have revealed principles about neural processing, in particular about vision. Previous works have demonstrated a direct correspondence between the hierarchy of human visual areas and layers of deep convolutional neural networks (DCNNs), suggesting that DCNN is a good model of visual object recognition in primate brain. Studying intracranial depth recordings allowed us to extend previous works by assessing when and at which frequency bands the activity of the visual system corresponds to the DCNN. Our key finding is that signals in gamma frequencies along the ventral visual pathway are aligned with the layers of DCNN. Gamma frequencies play a major role in transforming visual input to coherent object representations.
SArKS:de novodiscovery of gene expression regulatory motifs and domains by suffix array kernel smoothing
Authors: Wylie Dennis , Hofmann Hans A. , Zemelman Boris V. 
Published: May 2017

AbstractMotivationWe set out to develop an algorithm that can mine differential gene expression data to identify candidate cell type-specific DNA regulatory sequences. Differential expression is usually quantified as a continuous score—fold-change, test-statistic,p-value—comparing biological classes. Unlike existing approaches, ourde novostrategy, termed SArKS, applies nonparametric kernel smoothing to uncover promoter motifs that correlate with elevated differential expression scores. SArKS detects motifs by smoothing sequence scores over sequence similarity. A second round of smoothing over spatial proximity reveals multi-motif domains (MMDs). Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.ResultsWe applied SArKS to published gene expression data representing distinct neocortical neuron classes inM. musculusand interneuron developmental states inH. sapiens. When benchmarked against several existing algorithms for correlative motif discovery using a cross-validation procedure, SArKS identified larger motif sets that formed the basis for regression models with higher correlative power.Availabilityhttps://github.com/denniscwylie/sarks.Contactdenniswylie@austin.utexas.edu.Supplementary informationappended to document.
Relationality in negotiations: a systematic review and propositions for future research
Authors: Cheng Junjun , Huang Yimin , Su Yong 
Published: May 2017

PurposeThe purpose of this paper is to systematically review and analyze the important, yet under-researched, topic of relationality in negotiations and propose new directions for future negotiation research.Design/methodology/approachThis paper conducts a systematic review of negotiation literature related to relationality from multiple disciplines. Thirty-nine leading and topical academic journals are selected and 574 papers on negotiation are reviewed from 1990 to 2014. Based on the systematic review, propositions regarding the rationales for relationality in negotiations are developed and future research avenues in this area are discussed.FindingsOf 574 papers on negotiations published in 39 peer-reviewed journals between 1990 and 2014, only 18 papers have studied and discussed relationality in negotiations. This suggests that relationality as a theoretical theme has long been under-researched in negotiation research. For future research, this paper proposes to incorporate the dynamic, cultural and mechanism perspectives, and to use a qualitative approach to study relationality in negotiations.Originality/valueThis paper presents the first systematic review of the negotiation literature on relationality, and identifies new research topics on relationality in negotiations. In so doing, this research opens new avenues for future negotiation research on relationality.
Parents or peers, wealth or warmth? The impact of social support, wealth, and a positive outlook on self-efficacy and happiness
Authors: Aumeboonsuke Vesarach 
Published: May 2017

Purpose
The purpose of this paper is to investigate the association between family wealth, positive outlook, and support from significant others, including parents and friends, on self-efficacy and happiness.

Design/methodology/approach
The impact of family wealth, social support, and positive outlook on self-efficacy and one’s own happiness is analyzed through the partial least squared method.

Findings
There are five essential points that can be drawn from the statistical results. First, parents’ support tends to be more important than friends’ support for individuals’ happiness. Second, individuals that receive more support from parents tend to develop a higher level of self-efficacy. Third, individuals that are in a less wealthy family tend to develop a higher level of self-efficacy. Fourth, parents’ support plays a more important role in developing a higher level of self-efficacy for individuals that are in a less wealthy family than for individuals that are in a wealthier family. Finally, the positive link between happiness and self-efficacy was stronger for individuals in a wealthier family than for individuals in a less wealthy family.

Research limitations/implications
In particular, although individuals in a wealthier family tend to exhibit a lower level of self-efficacy, and happiness alone had no significant impact on self-efficacy, happiness significantly promoted self-efficacy more for individuals in a wealthier family than for individuals in a less wealthy family.

Social implications
In conclusion, the results from this research provide essential recommendations for individuals regarding the approach to happiness and self-efficacy. The results indicated how significant the role of parents’ support is in one’s happiness and that support from parents is more important for one’s self-efficacy and happiness than support from friends. Furthermore, individuals should be aware that money is not the ultimate answer for happiness and self-efficacy. Individuals in less wealthy families were able to enjoy a higher level of self-efficacy given that they were receiving sufficient support from their parents.

Originality/value
This study found that although individuals in a wealthier family tend to exhibit a lower level of self-efficacy, and happiness alone has no significant impact on self-efficacy, happiness significantly promote self-efficacy more for individuals in a wealthier family than for individuals in a less wealthy family. However, in the less-wealthier family, parents play more significant role and can generate high level of self-efficacy for their children.
Inequalities in economic and educational status among social groups in India
Authors: Awasthi Ishwar Chandra , Shrivastav Puneet Kumar 
Published: May 2017

Purpose
The purpose of this paper is to analyse the social and economic disparities across social groups in rural Uttar Pradesh. The paper demonstrates that the structure of the rural economy in India is characterised by deeply ingrained prejudices and social discrimination. The four-village study undertaken in one of the most populated states in India, Uttar Pradesh, clearly reveals that there is a huge disparity in terms of various social and economic indicators and that the so-called high growth has hardly helped in bettering their lives.

Design/methodology/approach
The paper is based on primary data collected from the Census survey of villages exploring socio-economic disparities across social groups by using decomposition models.

Findings
The results evidently lend credence to the postulations that a large proportion of the disadvantaged groups are prone to multiple deprivations, both in the society and in labour markets. The inquiry reveals this phenomenon clearly.

Research limitations/implications
From the policy point of view, it is therefore imperative to ensure the direct and focussed provision of basic human requirements in terms of education, employment and income of the state. The implementation of direct policy interventions is an absolute necessity if the state has to guarantee convergence and the inclusive growth process on a sustained basis.

Originality/value
This paper fulfils an identified need to study the inequality among the social groups in terms of education, employment, income and livelihood opportunities in selected villages of four districts of Uttar Pradesh.