bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hospital-level Variation in Utilization of Surgery for Clinical Stage I-II Pancreatic Adenocarcinoma
Authors: Swords Douglas S. , Mulvihill Sean J. , Skarda David E. , Finlayson Samuel R. G. , Stoddard Gregory J. , Ott Mark J. , Firpo Matthew A. , Scaife Courtney L. 
Published: July 2017

Objective:
To (1) evaluate rates of surgery for clinical stage I-II pancreatic ductal adenocarcinoma (PDAC), (2) identify predictors of not undergoing surgery, (3) quantify the degree to which patient- and hospital-level factors explain differences in hospital surgery rates, and (4) evaluate the association between adjusted hospital-specific surgery rates and overall survival (OS) of patients treated at different hospitals.

Background:
Curative-intent surgery for potentially resectable PDAC is underutilized in the United States.

Methods:
Retrospective cohort study of patients ≤85 years with clinical stage I-II PDAC in the 2004 to 2014 National Cancer Database. Mixed effects multivariable models were used to characterize hospital-level variation across quintiles of hospital surgery rates. Multivariable Cox proportional hazards models were used to estimate the effect of adjusted hospital surgery rates on OS.

Results:
Of 58,553 patients without contraindications or refusal of surgery, 63.8% underwent surgery, and the rate decreased from 2299/3528 (65.2%) in 2004 to 4412/7092 (62.2%) in 2014 (P < 0.001). Adjusted hospital rates of surgery varied 6-fold (11.4%–70.9%). Patients treated at hospitals with higher rates of surgery had better unadjusted OS (median OS 10.2, 13.3, 14.2, 16.5, and 18.4 months in quintiles 1–5, respectively, P < 0.001, log-rank). Treatment at hospitals in lower surgery rate quintiles 1–3 was independently associated with mortality [Hazard ratio (HR) 1.10 (1.01, 1.21), HR 1.08 (1.02, 1.15), and HR 1.09 (1.04, 1.14) for quintiles 1–3, respectively, compared with quintile 5] after adjusting for patient factors, hospital type, and hospital volume.

Conclusions:
Quality improvement efforts are needed to help hospitals with low rates of surgery ensure that their patients have access to appropriate surgery.
Cell-free andin vivocharacterization of Lux, Las, and Rpa quorum activation systems inE. coli
Authors: Halleran Andrew D. , Murray Richard M. 
Published: July 2017

AbstractSynthetic biologists have turned towards quorum systems as a path for building sophisticated microbial consortia that exhibit group decision making. Currently, however, even the most complex consortium circuits rely on only one or two quorum sensing systems, greatly restricting the available design space. High-throughput characterization of available quorum sensing systems is useful for finding compatible sets of systems that are suitable for a defined circuit architecture. Recently, cell–free systems have gained popularity as a test-bed for rapid prototyping of genetic circuitry.We take advantage of the transcription-translation cell-free system to characterize three commonly used Lux-type quorum activators, Lux, Las, and Rpa. We then compare the cell-free characterization to results obtainedin vivo.We find significant genetic crosstalk in both the Las and Rpa systems and substantial signal crosstalk in Lux activation. We show that cell-free characterization predicts crosstalk observedin vivo.
Toward leveraging big data in human functional connectomics: Generalization of brain graphs across scanners, sessions, and paradigms
Authors: Cao Hengyi , McEwen Sarah C. , Bearden Carrie E. , Addington Jean , Goodyear Bradley , Cadenhead Kristin S. , Mirzakhanian Heline , Cornblatt Barbara A. , Olvet Doreen M. , Mathalon Daniel H. , McGlashan Thomas H. , Perkins Diana O. , Belger Aysenil , Seidman Larry J. , Thermenos Heidi , Tsuang Ming T. , van Erp Theo G.M. , Walker Elaine F. , Hamann Stephan , Woods Scott W. , Cannon Tyrone D. 
Published: July 2017

AbstractWhile graph theoretical modeling has dramatically advanced our understanding of complex brain systems, the feasibility of aggregating brain graphic data in large imaging consortia remains unclear. Here, using a battery of cognitive, emotional and resting fMRI paradigms, we investigated the reproducibility of functional connectomic measures across multiple sites and sessions. Our results revealed overall fair to excellent reliability for a majority of measures during both rest and tasks, in particular for those quantifying connectivity strength, network segregation and network integration. Higher reliabilities were detected for cognitive tasks (vs rest) and for weighted networks (vs binary networks). While network diagnostics for several primary functional systems were consistently reliable independently of paradigm, those for cognitive-emotional systems were reliable predominantly when challenged by task. Different data aggregation approaches yielded significantly different reliability. In addition, we showed that after accounting for observed reliability, satisfactory statistical power can be achieved in the multisite context with a total sample size of approximately 250 when the effect size is at least moderate. Our findings provide direct evidence for the generalizability of brain graphs for both resting and task paradigms in large consortia and encourage the use of multisite, multisession scans to enhance power for human functional connectomic studies.
Predicting serious rare adverse reactions of novel chemicals
Authors: Poleksic Aleksandar , Xie Lei 
Published: July 2017

AbstractAdverse drug reactions (ADRs) are one of the main causes of death and a major financial burden on the world’s economy. Due to the limitations of the animal model, computational prediction of serious, rare ADRs is invaluable. However, current state-of-the-art computational methods do not yield significantly better predictions of rare ADRs than random guessing. We present a novel method, based on the theory of “compressed sensing”, which can accurately predict serious side-effects of candidate and market drugs. Not only is our method able to infer new chemical-ADR associations using existing noisy, biased, and incomplete databases, but our data also demonstrates that the accuracy of our approach in predicting a serious adverse reaction (ADR) for a candidate drug increases with increasing knowledge of other ADRs associated with the drug. In practice, this means that as the candidate drug moves up the different stages of clinical trials, the prediction accuracy of our method will increase accordingly. Thus, the compressed sensing based computational method reported here represents a major advance in predicting severe rare ADRs, and may facilitate reducing the time and cost of drug discovery and development.
Assessing Runs of Homozygosity: A comparison of SNP Array and Whole Genome Sequence low coverage data
Authors: Ceballos Francisco C. , Hazelhurst Scott , Ramsay Michèle 
Published: July 2017

AbstractRuns of Homozygosity (ROH) are sequences that arise when identical haplotypes are inherited from each parent. Since their first detection due to technological advances in the late 1990s, ROHs have been shedding light on human population history and deciphering the genetic basis of monogenic and complex traits and diseases. ROH studies have predominantly exploited SNP array data, but are gradually moving to whole genome sequence (WGS) data as it becomes available. WGS data, covering more genetic variability, can add value to ROH studies, but require additional considerations during analysis. Using SNP array and low coverage WGS data from 1885 individuals from 20 world populations, our aims were to compare ROH from the two datasets and to establish software conditions to get comparable results, thus providing guidelines for combining disparate datasets in joint ROH analyses. Using the PLINK Homozygosity functions, we found that by allowing 3 heterozygous SNPs per window when dealing with WGS low coverage data, it is possible to establish meaningful comparisons between data using the two technologies.
Geospatial statistics of high field functional MRI reveals topographical clustering for binocular stereo depth in early visual cortex
Authors: Parker A.J. , Coullon G. S. L. , Sanchez-Panchuelo R. M. , Francis S.T. , Clare S. , Kay D.A. , Duff E. P. , Minini L. , Jbabdi S. , Schluppeck D. , Bridge H. 
Published: July 2017

Significance statementFunctional topography is present throughout the cerebral cortex, often in the form of columns or clusters of neurons with similar functional properties within identified cortical regions. Most of the evidence for these structures comes from work with non-human species. Using high-field strength magnetic resonance imaging in living human cortex, the search for this structure is frustrated by the presence of a background of local spatial correlations in the signal across the cortical surface. This structured background, which we term ‘neural dust’, is a form of noise that imposes a fundamental limit on the detection of clustering and topography. We apply a novel analysis approach that quantifies the background of spatial correlations, so that we achieve reliable identification of high-signal clusters of activation in the human cortex at a scale previously only visible with invasive optical imaging in animals. We searched specifically in visual cortex for correlates of binocular stereoscopic depth. We show both that signals for stereoscopic depth are clustered into specific zones within the cortex and that these signals occur within spatially extended cortical domains, which have similar preferences for the stereoscopic depth. The revealed structures are reliably identified in all subjects tested and in repeated testing of individual subjects. Our methods provide an objective approach for defining the size and locations of clusters of activation within functional images of neural activity.AbstractA characteristic principle of the organization of cerebral neocortex is the presence of clusters or columns of neurons with similar functional properties. Animals with forward-facing eyes exploit slight differences between the images in the two eyes to determine binocular depth using stereopsis. Evidence for an organized structure in human visual cortex for the representation of stereoscopic depth has proved elusive. Using 7-tesla functional MRI, with gradient-echo echo-planar imaging at 0.75 mm isotropic resolution and a novel analytical approach based on geospatial mapping methods, we find that clustered responses for disparity-defined depth can be clearly segregated from a background of spatially correlated signals in all subjects tested. High-signal clusters are associated with cortical domains as large as 12-15mm across the cortical surface, in which nearby points in the cortical map tend to respond to the same stereoscopic depth. These domains are found predominantly within visual cortical area V3A.
Adaptive evolution of animal proteins over development: support for the Darwin selection opportunity hypothesis of Evo-Devo
Authors: Liu Jialin , Robinson-Rechavi Marc 
Published: July 2017

AbstractA driving hypothesis of Evo-Devo is that animal morphological diversity is shaped both by adaptation and by developmental constraints. Here we have tested Darwin’s “selection opportunity” hypothesis, according to which high evolutionary divergence in late development is due to strong positive selection. We contrasted it to a “developmental constraint” hypothesis, according to which late development is under relaxed negative selection. Indeed, the highest divergence between species, both at the morphological and molecular levels, is observed late in embryogenesis and post-embryonically. To distinguish between adaptation and relaxation hypotheses, we investigated the evidence of positive selection on protein-coding genes in relation to their expression over development, in flyDrosohila melanogaster, zebrafishDanio rerio, and mouseMus musculus. First, we found that genes specifically expressed in late development have stronger signals of positive selection. Second, over the full transcriptome, genes with evidence for positive selection trend to be expressed in late development. Finally, genes involved in pathways with cumulative evidence of positive selection have higher expression in late development. Overall, there is a consistent signal that positive selection mainly affects genes and pathways expressed in late embryonic development and in adult. Our results imply that the evolution of embryogenesis is mostly conservative, with most adaptive evolution affecting some stages of post-embryonic gene expression, and thus post-embryonic phenotypes. This is consistent with the diversity of environmental challenges to which juveniles and adults are exposed.
Socio-affective touch expression database
Authors: Lee Masson Haemy , Op de Beeck Hans 
Published: July 2017

AbstractSocio-affective touch communication conveys a vast amount of information about emotions and intentions in social contexts. In spite of the complexity of the socio-affective touch expressions we use daily, previous studies addressed only a few aspects of social touch mainly focusing on hedonics, such as stroking, leaving a wide range of social touch behaviour unexplored. To overcome this limit, we present the Socio-Affective Touch Expression Database (SATED), which includes a large range of dynamic interpersonal socio-affective touch events varying in valence and arousal. The original database contained 26 different social touch expressions each performed by three actor pairs. To validate each touch expression, we conducted two behavioural experiments investigating perceived naturalness and affective values. Based on the rated naturalness, 13 socio-affective touch expressions along with 12 corresponding non-social touch events were selected as a complete set, achieving 75 video clips in total. Moreover, we quantified motion energy for each touch expression to investigate its intrinsic correlations with perceived affective values and its similarity among actor-and action-pairs. As a result, the touch expression database is not only systematically defined and well-controlled, but also spontaneous and natural, while eliciting clear affective responses. This database will allow a fine-grained investigation of complex interpersonal socio-affective touch in the realm of social psychology and neuroscience along with potential application areas in affective computing and neighbouring fields.
Investigating the occurrence ofE. coliO157:H7 in the final effluents of two wastewater treatment plants
Authors: Osuolale Olayinka , Okoh Anthony 
Published: July 2017

AbstractAIMThe final effluent of two wastewater plants located in the Eastern Cape of South Africa were tested for the presence of Enterohaemorrhagic Escherichia coli O157:H7 (E. coli O157:H7) isolates, and characteristics of the isolates obtained were determined.METHODS AND RESULTSA total of 23 wastewater samples were collected from the treatment plants at the final effluent point after the disinfectant stages of wastewater processing. Altogether, 540 presumptive E. coli isolates were obtained by colony counting on the E. coli O157:H7 chromogenic agar base supplemented with cefixime tellurite and were sub-cultured onto sorbitol-MacConkey agar and tested for agglutination using the Prolex E. coli O157 latex test reagent kit. The results showed that the 149 suspected colonies from SMAC agar were all negative for the antisera.CONCLUSIONNone of the isolates agglutinated with antisera against E. coli O157. Thus no presence of the bacteria can be confirmed from the treated effluentsSIGNIFICANCE AND IMPACT OF STUDYThe likelihood of the receiving water body and the environment being contaminated with E. coli O157:H7 is therefore minimal.
Optical scanner assisted robotic assembly
Authors: Wojciechowski Jakub , Suszynski Marcin 
Published: July 2017

Purpose
This paper aims to propose the method of automatic robotic assembly of two or more parts placed without fixing instrumentation and positioning on the pallet.

Design/methodology/approach
Assembly tasks performed by industrial robots are usually based on a constant program, extensive tooling, fixing objects in a given place and a relatively limited sensory system. In this study, a different approach is presented. The industrial robot program is adjusted to the location of parts for assembly in the work space. This leads to a transition from a clearly defined assembly sequence realized by the industrial robot to the one in which the order of execution of the assembly operations can be determined by the mutual position of parts to be assembled.

Findings
The method presented in this study combines many already known algorithms. The contribution of the authors is to test and select the appropriate combination of methods capable of supporting robotic assembly process based on data from optical 3D scanners. The sequence of operations from scanning to place the parts in the installation position by an industrial robot is developed. A set of parameters for selected methods is presented. The result is a universal procedure that determines the position of the preset models in partial measurements performed at a fixed relative position of the sensor, the measurement object.

Originality/value
The developed procedure for determining the position of the parts is essential to develop a flexible robotic assembly system. It will be able to perform the task of assembly on the basis of appropriate search algorithms taking into account the selected and implemented sequence of assembly position and orientation of parts, particularly the base unit freely placed on an assembly pallete. It is also the basis of a system for testing different algorithms to optimize the flexible robotic assembly.
Investigation of ball screw’s alignment error based on dynamic modeling and magnitude analysis of worktable sensed vibration signals
Authors: Wang Yiqiang , Guo Zhengcai , Liu Botao , Zhu Yanfei , Luo Haibo 
Published: July 2017

Purpose
The alignment precision of existing methods is limited by the precision of detecting element and worker’s experience, which the parallelism between ball screw and guide way is not guaranteed effectively. Thus, this paper aims to propose a method of detecting ball screw’s alignment error (BSAE) via monitoring the average vibration magnitude induced by rotational frequency of ball screw (VMRFBS).

Design/methodology/approach
In this study, the ball screw is simplified as a freely supported beam. A mathematical model of the effect of BSAE on the contact angle of the ball and screw is established. The change of contact angle has effect on the deformation and contact stiffness according to the Hertz contact theory. To improve the accuracy of the experimental results, the VMRFBS are analyzed by using average method, and the average values of the VMRFBS at different BSAEs are calculated by using the least squares method.

Findings
The experimental results show that the average VMRFBS increases with the increasing of BSAE under the BSAE from 0 to 0.2 mm, while the other conditions are unchanged.

Originality/value
This method provides an approach to monitor the BSAE and improve the alignment accuracy of machine tools and automation equipment, which has a certain guide for improving the alignment accuracy of ball screw.
A hybrid technology for assembly sequence planning of reflector panels
Authors: Wang Dou , Shao Xiaodong , Ge Xiaobo , Liu Simeng 
Published: July 2017

Purpose
The purpose of this study is to guarantee assembly quality and reduce the number of manufacturing cycles required for an reflector of the large reflector antenna. An optimal approach combining a finite element method (FEM) with a genetic algorithm (GA) is developed to simulate and optimize reflector assembly before the assembly stage.

Design/methodology/approach
The chromosomes of GA are encoded with the consideration of the factors that affect the assembly of reflector. The fitness function of the GA consists of the assembly accuracy obtained from simulation, with evaluation of the assembly time consumption and labor cost. The algorithm will terminate when the GA is finished or the simulation results meet the permissible accuracy. Taking the assembly process of the reflector into account, an FEM based on a “life – death element” technique is introduced to quickly and precisely simulate reflector assembly.

Findings
A case study is presented, to which the proposed approach is applied. The results of finite element simulation demonstrate that the proposed FEM can simulate the reflector assembly process with oversimplified modeling and accurate simulation results. The optimal approach provides an accurate and efficient method for reflector assembly sequence planning indicated by the comparison of the measurements and calculation results.

Originality/value
The results also demonstrate that the proposed approach has practical significance for guiding reflector assembly in engineering practice.
Loan repayment performance of clients of informal lending institutions
Authors: Charles Goodluck , Mori Neema 
Published: July 2017

Purpose
The purpose of this article is to examine the effects that dynamic incentives and the borrowing histories of clients of informal lending institutions have on loan repayment performance, in particular, the extent to which multiple borrowing and progressive lending affect the repayment of loans.

Design/methodology/approach
The paper uses a data set of 835 borrowers drawn from an informal lending institution in Tanzania. Descriptive analysis and econometric models are used to test the developed hypotheses.

Findings
Whereas clients with multiple loans are associated with poor loan repayment, progressive lending contributes to positive repayment outcomes. Multiple borrowers face increased debt levels and thereby an increased inability to meet their repayment obligations; in contrast, progressive lending by building up a lender–client relationship helps clients to obtain higher loans with a minimum amount of screening.

Research limitations/implications
This was a cross-sectional study based on a sample of individual clients drawn from a single institution. However, since the majority of clients had also taken out loans with other financial institutions, the sample is considered to be representative.

Practical implications
A client’s past repayment performance and multiple loan history must be assessed so that multiple borrowing can be prevented and credit absorption capacity can be gauged more accurately. The repeated nature of the interactions and the threat to cut off any future lending (if loans are not repaid) can be exploited to overcome any information deficit.

Originality/value
This study was conducted in a context in which the degree of information sharing was low and institutional access to clients’ credit histories was limited. It contributes knowledge on how lenders minimise the risk flowing from the ex ante information gap and moral hazards arising from the ex post information gap.