bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retrospective attribution of false beliefs in 3-year-old children
Authors: Király Ildikó , Oláh Katalin , Csibra Gergely , Kovács Ágnes Melinda 
Published: October 2018

Significance
The continuous flow of social interactions requires humans to monitor others’ mental states dynamically, yet this aspect of mind reading remains largely neglected. We tested whether, beyond prospective belief tracking, young children would also attribute beliefs to others retrospectively. We found that 3-year-old children retrospectively inferred the content of someone’s beliefs by combining present information with relevant events retrieved from episodic memory. This finding shows that emerging capacities for episodic memory contribute to the development of social cognitive processes, enriching children’s ability to monitor others’ mental states.
Intergenerational transmission of paternal trauma among US Civil War ex-POWs
Authors: Costa Dora L. , Yetter Noelle , DeSomer Heather 
Published: October 2018

Significance
Understanding whether paternal trauma is transmitted to children to affect their longevity, the mechanisms behind any transmission, and the reversibility of paternal trauma can inform health interventions and increase our understanding of the persistence of health within families. We show that severe paternal hardship as a prisoner of war (POW) led to high mortality among sons, but not daughters, born after the war who survived to the age of 45 but that adequate maternal nutrition countered the effect of paternal POW trauma in a manner most consistent with epigenetic explanations. We are not aware of any large sample studies in human populations that examine the reversibility of paternal trauma nor the long-term impact of paternal ex-POW status on children.
Multistability of model and real dryland ecosystems through spatial self-organization
Authors: Bastiaansen Robbin , Jaïbi Olfa , Deblauwe Vincent , Eppinga Maarten B. , Siteur Koen , Siero Eric , Mermoz Stéphane , Bouvet Alexandre , Doelman Arjen , Rietkerk Max 
Published: October 2018

Significance
Today, vast areas of drylands in semiarid climates face the dangers of desertification. To understand the driving mechanisms behind this effect, many theoretical models have been created. These models provide insight into the resilience of dryland ecosystems. However, until now, comparisons with reality were merely visual. In this article, a systematic comparison is performed using data on wavenumber, biomass, and migration speed of vegetation patterns in Somalia. In agreement with reaction–diffusion models, a wide distribution of regular pattern wavenumbers was found in the data. This highlights the potential for extrapolating predictions of those models to real ecosystems, including those that elucidate how spatial self-organization of vegetation enhances ecosystem resilience.
In operando plasmonic monitoring of electrochemical evolution of lithium metal
Authors: Jin Yan , Zhou Lin , Yu Jianyu , Liang Jie , Cai Wenshan , Zhang Huigang , Zhu Shining , Zhu Jia 
Published: October 2018

Significance
In operando and nondestructive technology is urgently needed to monitor and further control lithium metal morphology evolution for reviving lithium metal batteries. Taking advantage of lithium plasmonics, we developed an in operando plasmonic monitoring platform to investigate lithium deposition behavior in different working conditions and varied electrolytes. This technology, with a well-established correlation between the evolving morphologies of lithium metal and in operando optical spectra, can serve as an effective platform for investigating lithium morphology during electrochemical operations, which can further speed up new electrolyte design and the development of alkali metal-based energy storage systems.
Mammalian behavior and physiology converge to confirm sharper cochlear tuning in humans
Authors: Sumner Christian J. , Wells Toby T. , Bergevin Christopher , Sollini Joseph , Kreft Heather A. , Palmer Alan R. , Oxenham Andrew J. , Shera Christopher A. 
Published: October 2018

Significance
Sound consists of a dynamic stream of energy at different frequencies. Auditory processing of sound frequency is critical in determining our ability to interact and communicate in a complex acoustic world, yet fundamental gaps remain in our understanding of how this is achieved. Indeed, the resolving power of the system, how best to measure it, and the mechanisms that underlie it are all still debated. Here, we provide critical evidence demonstrating that humans can resolve the frequency components of competing sounds better than other commonly studied mammals. This finding raises important questions both for theories of auditory perception and for our understanding of the evolutionary relationships between the auditory system and acoustic communication, including speech.
Collective decision making by rational individuals
Authors: Mann Richard P. 
Published: October 2018

Significance
Humans and animals use the decisions they observe others making as valuable information about the quality of potential choices. We anticipate that behavioral rules that better approximate the decisions of a rational, expected fitness-maximizing agent will be favored by natural selection. In this paper I show that many aspects of collective decision making can be predicted through considering what a rational agent would do. I also show that a theory of strictly rational agents explains much of the variability between and within species and makes sometimes counterintuitive predictions that can be experimentally tested. Most importantly, my model shows that how collective decision making is observed and measured is critically important in interpreting and understanding behavior.
ADP-ribosyl–binding and hydrolase activities of the alphavirus nsP3 macrodomain are critical for initiation of virus replication
Authors: Abraham Rachy , Hauer Debra , McPherson Robert Lyle , Utt Age , Kirby Ilsa T. , Cohen Michael S. , Merits Andres , Leung Anthony K. L. , Griffin Diane E. 
Published: October 2018

Significance
Alphaviruses are mosquito-borne RNA viruses that cause encephalitis, rash, and arthritis. Alphavirus nonstructural protein 3 (nsP3) has a highly conserved macrodomain that can bind and remove ADP-ribose (ADPr) residues from ADP-ribosylated proteins, but its role in virus replication was not known. We show that alphavirus replication in neural cells depends on protein ADP ribosylation and that nsP3s with mutations that eliminate ADPr binding cannot form a functional replicase. Mutations that decrease ADPr binding result in fewer infected cells, while mutations that increase binding but decrease hydrolase activity infect cells normally but amplify replication complexes less well. Therefore, alphavirus replication requires nsP3 macrodomain interaction with one or more ADP-ribosylated proteins, as is consistent with the observed high conservation of this region.
Microbiome-assisted carrion preservation aids larval development in a burying beetle
Authors: Shukla Shantanu P. , Plata Camila , Reichelt Michael , Steiger Sandra , Heckel David G. , Kaltenpoth Martin , Vilcinskas Andreas , Vogel Heiko 
Published: October 2018

Significance
Ephemeral diets such as carrion are high-quality resources that are susceptible to microbial spoilage. Carrion-feeding insects that breed on decaying carcasses must overcome challenges arising from competing microbes. Here we report that a carrion-feeding burying beetle preserves carcasses by regulating its microbial growth, resulting in changes in its biochemical properties including the reduction of toxic polyamines associated with putrefaction and nutrient loss. The beetle’s microbial symbionts form a biofilm-like matrix on carcasses, which is important for optimal larval development. The beetles and their microbiome thus coordinate a specialized adaptive strategy of carrion management, enabling them to preserve carrion quality and support larval growth in a challenging resource such as carrion.
Control of movement vigor and decision making during foraging
Authors: Yoon Tehrim , Geary Robert B. , Ahmed Alaa A. , Shadmehr Reza 
Published: October 2018

Significance
How long should one stay and accumulate reward, and then, how fast should one travel to the next reward site? Marginal value theorem describes the decision-making process: the brain compares the immediate rate of harvest with its global history of capture, deciding to leave when the immediate rate falls below the average. Here, we extended the theory, showing that the same principle can be used to control speed of movements: the brain should compare the immediate rate of energy expenditure during movement with the global capture rate, planning to arrive at the destination when the two become equal. Experimental results confirmed many of the predictions, suggesting that a shared principle may underlie decision making and control of movement vigor.
Proximity-enhanced SuFEx chemical cross-linker for specific and multitargeting cross-linking mass spectrometry
Authors: Yang Bing , Wu Haifan , Schnier Paul D. , Liu Yansheng , Liu Jun , Wang Nanxi , DeGrado William F. , Wang Lei 
Published: October 2018

Significance
Chemical cross-linking mass spectrometry is a powerful method to identify protein interaction partners. The cross-links also provide approximate interresidue distances, which can help model the structures of complexes. However, current cross-linking reagents react with only a limited set of amino acid residues and their very high reactivity can induce cross-links between sites that are distant in the native state of the interrogated proteins. We therefore developed a “plant-and-cast” strategy, in which a heterobifunctional cross-linker is “planted” onto surface Lys residues using a highly reactive succinimide ester. The half-reacted cross-linker then “casts” a much less reactive sulfonyl fluoride across the proximal surface resulting in cross-links to neighboring Ser, Thr, Tyr, His, or Lys sidechains in a proximity-enhanced reaction.
Relation between blood pressure and pulse wave velocity for human arteries
Authors: Ma Yinji , Choi Jungil , Hourlier-Fargette Aurélie , Xue Yeguang , Chung Ha Uk , Lee Jong Yoon , Wang Xiufeng , Xie Zhaoqian , Kang Daeshik , Wang Heling , Han Seungyong , Kang Seung-Kyun , Kang Yisak , Yu Xinge , Slepian Marvin J. , Raj Milan S. , Model Jeffrey B. , Feng Xue , Ghaffari Roozbeh , Rogers John A. , Huang Yonggang 
Published: October 2018

Significance
Continuous, cuffless, and noninvasive blood pressure monitoring by measuring the pulse wave velocity is generally considered to be a promising technique for noninvasive measurements. Previously reported relations between blood pressure and pulse wave velocity relation involve unrealistic assumptions that do not hold for human arteries, and also rely on empirical expressions without any theoretical basis. Here, an analytical model without such assumptions or empirical expressions is established to yield a relation between blood pressure and pulse wave velocity that has general utility for future work in continuous, cuffless, and noninvasive blood pressure monitoring.
Identification of the Optimal Recipient Layer for Transplanted Fat: A Prospective Study on Breast Lipoaugmentation
Authors: Guo Xiaoshuang , Mu Dali , Xing Wenshan , Qu Yaping , Luan Jie 
Published: October 2018

Abstract

Background
Fat grafting has become a popular procedure in aesthetic and reconstructive surgeries due to its safety, minimal invasiveness, and favorable visual outcomes, although the volume retention rate is unpredictable.

Objectives
A prospective clinical study on lipoaugmentation of the breast was conducted to compare fat retention rates in the pectoralis muscle and the periglandular area.

Methods
This prospective study included 20 breasts from 11 patients who underwent primary lipoaugmentation. Volume retention rate and percentage augmentation among different recipient layers, as well as complications and patient satisfaction, were evaluated. Magnetic resonance imaging was performed preoperatively and at 1 day and 3 months postoperatively. Complications were recorded, and patient satisfaction was appraised through the use of the Breast-Q questionnaire.

Results
Breasts were injected with 207 ± 29 mL of fat, achieving overall volume retention rates of 56.63% ± 16.40%. The overall augmentation was 21.53% ± 10.27%. Volume retention rate was significantly higher (59.00% ± 13.84%) in the periglandular area than in the pectoralis muscle (47.21% ± 22.41%) (P = 0.04). Augmentation was significantly higher (32.13% ± 12.96%) in the periglandular area than in the pectoralis muscle (4.95% ± 4.23%) (P = 0.00). Pain and numbness were the only reported complications. The Breast-Q score increased significantly for the measures “satisfaction with breasts,” “psychosocial well-being,” and “sexual well-being.”

Conclusions
Fat transfer is a safe and acceptable method for aesthetic and reconstructive breast surgery. The periglandular area was a better recipient site than muscle for transferred fat.

Level of Evidence: 4
Integrative cancer patient stratification via subspace merging
Authors: Ding Hao , Sharpnack Michael , Wang Chao , Huang Kun , Machiraju Raghu 
Published: October 2018

Abstract

Motivation
Technologies that generate high-throughput omics data are flourishing, creating enormous, publicly available repositories of multi-omics data. As many data repositories continue to grow, there is an urgent need for computational methods that can leverage these data to create comprehensive clusters of patients with a given disease.

Results
Our proposed approach creates a patient-to-patient similarity graph for each data type as an intermediate representation of each omics data type and merges the graphs through subspace analysis on a Grassmann manifold. We hypothesize that this approach generates more informative clusters by preserving the complementary information from each level of omics data. We applied our approach to The Cancer Genome Atlas (TCGA) breast cancer dataset and show that by integrating gene expression, microRNA and DNA methylation data, our proposed method can produce clinically useful subtypes of breast cancer. We then investigate the molecular characteristics underlying these subtypes. We discover a highly expressed cluster of genes on chromosome 19p13 that strongly correlates with survival in TCGA breast cancer patients and validate these results in three additional breast cancer datasets. We also compare our approach with previous integrative clustering approaches and obtain comparable or superior results.

Availability and implementation
https://github.com/michaelsharpnack/GrassmannCluster

Supplementary information
Supplementary data are available at Bioinformatics online.
farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods
Authors: Wang Zhe , Wang Xuwen , Li Youyong , Lei Tailong , Wang Ercheng , Li Dan , Kang Yu , Zhu Feng , Hou Tingjun 
Published: October 2018

Abstract

Summary
Protein-protein interactions (PPIs) have been regarded as an attractive emerging class of therapeutic targets for the development of new treatments. Computational approaches, especially molecular docking, have been extensively employed to predict the binding structures of PPI-inhibitors or discover novel small molecule PPI inhibitors. However, due to the relatively ‘undruggable’ features of PPI interfaces, accurate predictions of the binding structures for ligands towards PPI targets are quite challenging for most docking algorithms. Here, we constructed a non-redundant pose ranking benchmark dataset for small-molecule PPI inhibitors, which contains 900 binding poses for 184 protein-ligand complexes. Then, we evaluated the performance of MM/PB(GB)SA approaches to identify the correct binding poses for PPI inhibitors, including two Prime MM/GBSA procedures from the Schrödinger suite and seven different MM/PB(GB)SA procedures from the Amber package. Our results showed that MM/PBSA outperformed the Glide SP scoring function (success rate of 58.6%) and MM/GBSA in most cases, especially the PB3 procedure which could achieve an overall success rate of ∼74%. Moreover, the GB6 procedure (success rate of 68.9%) performed much better than the other MM/GBSA procedures, highlighting the excellent potential of the GBNSR6 implicit solvation model for pose ranking. Finally, we developed the webserver of Fast Amber Rescoring for PPI Inhibitors (farPPI), which offers a freely available service to rescore the docking poses for PPI inhibitors by using the MM/PB(GB)SA methods.

Availability and implementation
farPPI web server is freely available at http://cadd.zju.edu.cn/farppi/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical
Authors: Zahn Matthew , Adalja Amesh A , Auwaerter Paul G , Edelson Paul J , Hansen Gail R , Hynes Noreen A , Jezek Amanda , MacArthur Rodger D , Manabe Yukari C , McGoodwin Colin , Duchin Jeffrey S 
Published: October 2018

Abstract
Infectious diseases (ID) physicians play a crucial role in public health in a variety of settings. Unfortunately, much of this work is undercompensated despite the proven efficacy of public health interventions such as hospital acquired infection prevention, antimicrobial stewardship, disease surveillance, and outbreak response. The lack of compensation makes it difficult to attract the best and the brightest to the field of ID, threatening the future of the ID workforce. Here, we examine compensation data for ID physicians compared to their value in population and public health settings and suggest policy recommendations to address the pay disparities that exist between cognitive and procedural specialties that prevent more medical students and residents from entering the field. All ID physicians should take an active role in promoting the value of the subspecialty to policymakers and influencers as well as trainees.
The Impact of a National Antimicrobial Stewardship Program on Antibiotic Prescribing in Primary Care: An Interrupted Time Series Analysis
Authors: Balinskaite Violeta , Johnson Alan P , Holmes Alison , Aylin Paul 
Published: October 2018

Abstract

Background
The Quality Premium was introduced in 2015 to financially reward local commissioners of healthcare in England for targeted reductions in antibiotic prescribing in primary care.

Methods
We used a national antibiotic prescribing dataset from April 2013 until February 2017 to examine the number of antibiotic items prescribed, the total number of antibiotic items prescribed per STAR-PU (specific therapeutic group age/sex-related prescribing units), the number of broad-spectrum antibiotic items prescribed, and broad-spectrum antibiotic items prescribed, expressed as a percentage of the total number of antibiotic items. To evaluate the impact of the Quality Premium on antibiotic prescribing, we used a segmented regression analysis of interrupted time series data.

Results
During the study period, over 140 million antibiotic items were prescribed in primary care. Following the introduction of the Quality Premium, antibiotic items prescribed decreased by 8.2%, representing 5933563 fewer antibiotic items prescribed during the 23 post-intervention months, as compared with the expected numbers based on the trend in the pre-intervention period. After adjusting for the age and sex distribution in the population, the segmented regression model also showed a significant relative decrease in antibiotic items prescribed per STAR-PU. A similar effect was found for broad-spectrum antibiotics (comprising 10.1% of total antibiotic prescribing), with an 18.9% reduction in prescribing.

Conclusions
This study shows that the introduction of financial incentives for local commissioners of healthcare to improve the quality of prescribing was associated with a significant reduction in both total and broad-spectrum antibiotic prescribing in primary care in England.
The Surface Quasi-geostrophic Equation With Random Diffusion
Authors: Buckmaster Tristan , Nahmod Andrea , Staffilani Gigliola , Widmayer Klaus 
Published: October 2018

Abstract
Consider the surface quasi-geostrophic equation with random diffusion, white in time. We show global existence and uniqueness in high probability for the associated Cauchy problem satisfying a Gevrey type bound. This article is inspired by a recent work of Glatt-Holtz and Vicol [16].
Immunotherapy-related adverse events (irAEs): extraction from FDA drug labels and comparative analysis
Authors: Wang QuanQiu , Xu Rong 
Published: October 2018

Abstract

Objectives
Immune checkpoint inhibitors (ICIs) have dramatically improved outcomes in cancer patients. However, ICIs are associated with significant immune-related adverse events (irAEs) and the underlying biological mechanisms are not well-understood. To ensure safe cancer treatment, research efforts are needed to comprehensively detect and understand irAEs.

Materials and methods
We manually extracted and standardized irAEs from The U.S Food and Drug Administration (FDA) drug labels for six FDA-approved ICIs. We compared irAE profile similarities among ICIs and 1507 FDA-approved non-ICI drugs. We investigated how irAEs have differential effects on human organs by classifying irAEs based on their targeted organ systems. Finally, we identified broad-spectrum (nontarget-specific) and narrow-spectrum (target-specific) irAEs.

Results
A total of 893 irAEs were extracted. 31.4% irAEs were shared among ICIs as compared to the 8.0% between ICIs and non-ICI drugs. irAEs were resulted from both on- and off-target effects: irAE profiles were more similar for ICIs with same target than different targets, demonstrating the on-target effects; irAE profile similarity for ICIs with the same target is less than 50%, demonstrating unknown off-target effects. ICIs significantly target many organ systems, including endocrine system (3.4-fold enrichment), metabolism (3.7-fold enrichment), immune system (3.6-fold enrichment), and autoimmune system (4.8-fold enrichment). We identified 21 broad-spectrum irAEs shared among all ICIs, 20 irAEs specific for PD-L1/PD-1 inhibition, and 28 irAEs specific for CTLA-4 inhibition.

Discussion and conclusion
Our study presents the first effort toward building a standardized database of irAEs. The extracted irAEs can serve as the gold standard for automatic irAE extractions from other data resources and set a foundation to understand biological mechanisms of irAEs.