bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulostat Inferelator: a novel network biology platform to uncover molecular devices that predetermine cellular response phenotypes
Authors: Ung Choong Yong , Ghanat Bari Mehrab , Zhang Cheng , Liang Jingjing , Correia Cristina , Li Hu 
Published: May 2019

Abstract
With the emergence of genome editing technologies and synthetic biology, it is now possible to engineer genetic circuits driving a cell's phenotypic response to a stressor. However, capturing a continuous response, rather than simply a binary ‘on’ or ‘off’ response, remains a bioengineering challenge. No tools currently exist to identify gene candidates responsible for predetermining and fine-tuning cell response phenotypes. To address this gap, we devised a novel Regulostat Inferelator (RSI) algorithm to decipher intrinsic molecular devices or networks that predetermine cellular phenotypic responses. The RSI algorithm is designed to extract gene expression patterns from basal transcriptomic data in order to identify ‘regulostat’ constituent gene pairs, which exhibit rheostat-like mode-of-cooperation capable of fine-tuning cellular response. Our proof-of-concept study provides computational evidence for the existence of regulostats and that these networks predetermine cellular response prior to exposure to a stressor or drug. In addition, our work, for the first time, provides evidence of context-specific, drug–regulostat interactions in predetermining drug response phenotypes in cancer cells. Given RSI-inferred regulostat networks offer insights for prioritizing gene candidates capable of rendering a resistant phenotype sensitive to a given drug, we envision that this tool will be of great value in bioengineering and medicine.
Structures and mechanism of transcription initiation by bacterial ECF factors
Authors: Fang Chengli , Li Lingting , Shen Liqiang , Shi Jing , Wang Sheng , Feng Yu , Zhang Yu 
Published: May 2019

Abstract
Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 Å of Escherichia coli transcription initiation complex comprising σE—the most-studied bacterial ECF σ factor (Ec σE-RPo), and a crystal structure at 3.1 Å of Mycobacterium tuberculosis transcription initiation complex with a chimeric σH/E (Mtb σH/E-RPo). The structure of Ec σE-RPo reveals key interactions essential for assembly of E. coli σE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli σE. Moreover, both structures show that the non-conserved linkers (σ2/σ4 linker) of the two ECF σ factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF σ factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such σ2/σ4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF σ factors-mediated transcription initiation.
Update on hypoparathyroidism
Authors: Cusano Natalie E. , Bilezikian John P. 
Published: May 2019

Purpose of review
Hypoparathyroidism is a rare endocrine disorder characterized by low or insufficient parathyroid hormone (PTH) concentrations leading to hypocalcemia, hyperphosphatemia, and markedly reduced bone turnover. Despite being a rare disease, hypoparathyroidism has a profound impact on affected patients.

Recent findings
Recent epidemiologic surveys demonstrate a prevalence of between 5.3 and 40/100 000, confirming the orphan status of this disease. There is a female predominance, and anterior neck surgery is the most common etiology. Recent studies have better elucidated the chronic manifestations of the disease, impacting quality of life and multiple organ systems including the renal, cardiovascular, and skeletal systems. There are now data on longer term use of parathyroid hormone (PTH) and PTH analogs.

Summary
This review focuses on recent contributions to the literature on the prevalence and epidemiology of the disease, risk of chronic manifestations, and treatment with PTH(1-34) and rhPTH(1-84). Further research is needed to determine the pathophysiology of complications in hypoparathyroidism and whether interventions can decrease future risk of these complications. In addition, further data are needed with regards to more physiologic dosing regimens and long-term treatment with PTH and PTH analogs.
Differences in Consumer Assessment of Healthcare Providers and Systems Clinician and Group Survey Scores by Recency of the Last Visit
Authors: Setodji Claude M. , Burkhart Q. , Hays Ron D. , Quigley Denise D. , Skootsky Samuel A. , Elliott Marc N. 
Published: May 2019

Background:
Patient experience data can be collected by sampling patients periodically (eg, patients with any visits over a 1-year period) or sampling visits continuously (eg, sampling any visit in a monthly interval). Continuous sampling likely yields a sample with more frequent and more recent visits, possibly affecting the comparability of data collected under the 2 approaches.

Objective:
To explore differences in Consumer Assessment of Healthcare Providers and Systems Clinician and Group survey (CG-CAHPS) scores using periodic and continuous sampling.

Research Design:
We use observational data to estimate case-mix–adjusted differences in patient experience scores under 12-month periodic sampling and simulated continuous sampling.

Subjects:
A total of 29,254 adult patients responding to the CG-CAHPS survey regarding visits in the past 12 months to any of 480 physicians, 2007–2009.

Measures:
Overall doctor rating and 4 CG-CAHPS composite measures of patient experience: doctor communication, access to care, care coordination, and office staff.

Results:
Compared with 12-month periodic sampling, simulated continuous sampling yielded patients with more recent visits (by definition), more frequent visits (92% of patients with 2+ visits, compared with 76%), and more positive case-mix–adjusted CAHPS scores (2–3 percentage points higher).

Conclusions:
Patients with more frequent visits reported markedly higher CG-CAHPS scores, but this causes only small to moderate changes in adjusted physician-level scores between 12-month periodic and continuous sampling schemes. Caution should be exercised in trending or comparing scores collected through different schemes.
Characteristics of hardware failure in patients undergoing surgical stabilization of rib fractures: A Chest Wall Injury Society multicenter study
Authors: Sarani Babak , Allen Rebecca , Pieracci Fredric M. , Doben Andrew R. , Eriksson Evert , Bauman Zachary M. , Gupta Puneet , Semon Greg , Greiffenstein Patrick , Chapman Alistair J. , Kim Brian D. , Lottenberg Lawrence , Gardner Scott , Marasco Silvana , White Tom 
Published: May 2019

BACKGROUND
Surgical stabilization of rib fractures (SSRF) is increasingly used for severe rib fractures/flail chest. There are no reports discussing mechanisms of failure of implanted hardware, its clinical presentation, or consequences. The purpose of this study was to evaluate the incidence, presenting signs, and clinical sequela of hardware failure after SSRF.

METHODS
A multicenter, retrospective study was performed by a group of surgeons with a large SSRF case volume. All cases with known hardware failure from January 1, 2010, to December 31, 2017, were included. The surgeon's experience at the time of hardware implantation, specific implant used, number of failures the surgeon had experienced with the same system, and time from implantation to hardware failure were recorded. Additionally, patient demographics, including age, comorbid conditions, and number and location of rib fractures were recorded. Symptomatology associated with hardware failure and need for explant and/or reimplantation of hardware was also recorded. Nonparametric statistical tests were used to compare cohorts.

RESULTS
Of 1,224 patients who underwent SSRF, 38 patients with 233 rib fractures and 279 fracture segments experienced hardware failure and were enrolled in the study. Twelve patients presented more than 3 months following injury. Median age was 54 years old and 34% were active smokers. One hundred forty-four plates were implanted with a median of four plates per patient. Median number of SSRF cases by each surgeon was 100 (range, 1–280). Fractures and hardware failure were most frequent in the anterolateral/lateral region. Hardware failure was mostly due to screw migration and plate fracture. Hardware failure was asymptomatic in 40% and presented as pain in 42% of cases. Fifty-five percent of the cases required explantation of hardware, and only 10% required SSRF again. There was no difference between the acute and chronic fracture cohorts.

CONCLUSION
Hardware failure after SSRF is rare and often asymptomatic. When present, it rarely requires redo SSRF.

LEVEL OF EVIDENCE
Therapeutic, level V.
Inhibition of ADORA1 attenuates hepatic steatosis by gut microbiotaderived acetic acid fromAstragaluspolysaccharides
Authors: Hong Ying , Zheng Ningning , He Xuyun , Zhong Jing , Ma Junli , Zhao Aihua , Zheng Xiaojiao , Gu Yu , Yao Jian , Li Yue , Yuan Lin , Lin Min , Lu Xiong , Ping Jinliang , Song Pengtao , Li Bingbing , Han Ruiting , Sheng Lili , Zhang Weidong , Ding Kan , Liu Jun , Jia Wei , Li Houkai 
Published: May 2019

AbstractThe authors have withdrawn this manuscript, because some data could not be replicated. During the process of subsequent revision of the manuscript, we separated the data into two parts. The majority data of the preprint draft, the anti-NAFLD effect ofAstragaluspolysaccharides (APS) in mice and the contribution of gut microbiota, were independently published in 2021 after substantial revision (doi:https://doi.org/10.1080/19490976.2021.1930874). However, the data on figure 6 (about ARs inhibitors DPCPX orally ameliorating NAFLD in mice, andAdora1si-RNA datain vitro) could not be fully replicated in subsequent experiments. The most probable reason might be due to the batch differences of mice / cells, or other undetermined factors during experiment. Moreover, we have carried out in-depth studies on the exact role of hepatic A1R on NAFLD formation, which is opposite to our prior assumption. Therefore, we do not wish this work to be cited as reference for the project. We apologize for any inconvenience caused to our readers. Any questions can be addressed to first/corresponding author.
Sir2 is essential for intergenerational effects of parental diet on offspring metabolism in Drosophila
Authors: Hayashi Ryoya , Takeo Satomi , Aigaki Toshiro 
Published: May 2019

AbstractRecent studies have revealed that parental diet can affect offspring metabolism and longevity in Drosophila. However, the underlying mechanisms are still unknown. Here we demonstrate that Sir2 encoding an NAD+-dependent histone deacetylase is required for the intergenerational effects of low nutrition diet (1:5 dilution of standard diet). We observed an increased amount of triacylglyceride (TAG) in the offspring when fathers were maintained on a low nutrition diet for 2 days. The offspring had increased levels of metabolites of glycolysis and TCA cycle, the primary energy producing pathways. We found that Sir2 mutant fathers showed no intergenerational effects. RNAi-mediated knockdown of Sir2 in the fat body was sufficient to mimic the Sir2 mutant phenotype, and the phenotype was rescued by transgenic expression of wild-type Sir2 in the fat body. Interestingly, even fathers had no experience of low nutrition diet, overexpression of Sir2 in their fat bodies induced a high level of TAG in the offspring. These findings indicated that Sir2 is essential in the fat body of fathers to induce intergenerational effects of low nutrition diet.
Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients
Authors: Lou Shaoke , Li Tianxiao , Spakowicz Daniel , Chupp Geoffrey Lowell , Gerstein Mark 
Published: May 2019

AbstractThe pathogenesis of asthma is a complex process involving multiple genes and pathways. Identifying biomarkers from asthma datasets, especially those that include heterogeneous subpopulations, is challenging. In this work, we developed a framework that incorporates a denoising autoencoder and a supervised learning approach to identify gene signatures related to asthma severity. The autoencoder embeds high-dimensional gene expression data into a lower-dimensional latent space in an unsupervised fashion, enabling us to extract distinguishing features from gene expression data. We found that the weights on hidden units in this latent space correlate well with previously defined and clinically relevant clusters of patients. Moreover, pathway analysis based on each gene’s contribution to the hidden units showed significant enrichment in known asthma-related pathways. We then used genes that contribute most to the hidden units to develop a secondary supervised classifier (based on random forest) for directly predicting asthma severity. The random-forest importance metric from this classifier identified a signature based on 50 key genes, which can predict severity with an AUROC of 0.81 and thus have potential as diagnostic biomarkers. Furthermore, the key genes could also be used for successfully estimating, via support-vector-machine regression, the FEV1/FVC ratios across patients, achieving pre- and post-treatment correlations of 0.56 and 0.65, respectively (between predicted and observed values). The 50 biomarker candidate genes can be found in supplementary. The source codes are freely available upon request.
Investigating the impact of religious commitment on purchase of self-expressive brand products
Authors: Mirkhah Seyedeh Maryam , Karami Nasser 
Published: May 2019

Purpose
Brand and religion, although seemingly irrelevant, are sometimes considered as competitors in satisfying certain consumer needs. The purpose of this paper is to explore the link between religious commitment and purchase of self-expressive (SE) brand products in the context of the Iranian consumer market. Furthermore, this paper investigates the effect of religious commitment on consumers’ brand recall for Western versus local brand products.

Design/methodology/approach
Distributing questionnaires was used to collect primary data. Use of statistical techniques, specifically inferential and descriptive statistics were used through SPSS software.

Findings
Study 1 findings support that there is a strong link between religious commitment and purchase of SE brand products; the more the consumers’ religiosity, the less their preference for SE brand products. The results of Study 2 illustrate that there is no meaningful link between the religious commitment of individuals and their brand recall for Western products. Furthermore, there are key correlations between religious commitment and gender and also between brand purchase and age and brand purchase and income.

Research limitations/implications
The results help domestic and international marketers form a better understanding of consumers’ behavior regarding SE brand products and brand recall depending on consumers’ religious commitment. The findings also assist marketers and brand managers in designing more effective advertisements and branding strategies based on their chosen target consumer market.

Originality/value
Little research has examined the relationship between religiosity and its effect on the purchase of brand products; this is the first academic study analyzing the effect of commitment to Islam on purchase behavior of SE brand products in the context of the Islamic consumer market.
Clients’ perspectives on therapists who build family and personal harmony
Authors: Yap‐Tan Patricia Michelle Eng Hui , Foo Magdalene Tze Suang 
Published: May 2019

Our theory of harmony therapy explains how therapists have helped disharmonious families or couples build relational harmony without sacrificing intrapersonal harmony. In collectivist Singapore, where the family is the basic unit of society, and racial and religious harmony is the dominant discourse, therapists may worry that family harmony is valued so much that individuals’ intrapersonal harmony might be sidelined. We used grounded theory to guide our interviewee selection and qualitative analysis of thirty clients who sought therapy to find harmony in their conflictual relationships. Clients perceived that therapists who built both family and intrapersonal harmony (1) were helpful professionals, (2) encouraged collaborative conversations, (3) had expertise, (4) were more involved than usual, and (5) were collaborative experts. Therapy was perceived as less effective due to (a) insufficient or unhelpful expertise, (b) insufficient or unhelpful involvement, and (c) perceptions of unhelpful professionalism.Practitioner points

We aim to build interpersonal harmony without sacrificing intrapersonal harmony with families from collectivistic cultures

This means owning our professionalism and expertise with clients lightly, as both can sometimes be experienced as unhelpful

We encourage collaborative conversations, which are rarely experienced as unhelpful

We want to ensure that clients feel we are sufficiently involved with them and sometimes go ‘beyond the ordinary’
Geriatric medicine services for older surgical patients in acute hospitals: Results from a binational survey
Authors: Thillainadesan Janani , Hilmer Sarah , Close Jacqui , Kearney Leanne , Naganathan Vasi 
Published: May 2019

AbstractObjectiveTo describe perioperative geriatric medicine services in Australia and New Zealand, and to explore geriatricians’ views on the need for and challenges in providing perioperative care.MethodAn electronic questionnaire was sent to heads of geriatric medicine departments.ResultsSixty‐seven (83%) of 81 identified geriatric medicine departments responded. Twelve (18%) departments provide a proactive surgical‐geriatric medicine service. Their most common features were regular geriatric medicine ward rounds (100%), medication review (92%) and attendance at multidisciplinary meetings (83%). All respondents thought there was a need for geriatric medicine to provide greater input into the care of older surgical patients. Lack of funding (88%) and not enough geriatricians (58%) were the major perceived barriers.ConclusionsAlthough geriatricians believe they should provide proactive collaborative care for older surgical patients, only a few hospitals currently provide these services. Funding streams for these services and further research to determine the best models of care are needed.
Getting Their Way: Bias and Deference to Trial Courts
Authors: Hübert Ryan 
Published: May 2019

AbstractHow much do trial judges influence the law in the United States? I analyze a model of adjudication by a trial judge who engages in fact finding before deciding a case, but whose decision may be reversed. The model makes three broad points. First, it provides an informational rationale for ex post deference to biased trial judges that does not require an ex ante commitment by an appellate court to a standard of review. Second, it shows how procedural discretion can bring biased trial judges' rulings closer to appellate doctrine despite enabling trial judges to “get their way” more often. Third, de facto law as represented by trial judges' case‐by‐case adjudication will differ substantially from de jure law. As long as there are not too many extremist trial judges, de facto law will reflect the predispositions of trial judges, not legal doctrine.
“What Are We Doing to These Shoshone People?”: The Ontological Politics of a Shoshone Grinding Stone
Authors: Morini Ryan S. 
Published: May 2019

ABSTRACTThis article shares the story of an octogenarian Western Shoshone (Newe) elder who removed a grinding stone from an archaeological dig in protest and was threatened with federal fines and jail time. She shared a video recording of the incident and her correspondence with federal agencies in the interest of making her story known more widely. In this article, I unpack the politics of heritage management in this settler colonial context, using extended quotations so that the Newe involved serve as the primary theorists and analysts of the situation and its significance to Newe heritage. Through this approach, we get a glimpse of how some Newe elders have experienced anthropology and heritage management in practice, exposing power relations entangling anthropology through its utility in dealing with issues of heritage. [survivance, decolonizing anthropology, critical heritage management, Indigenous archaeologies]
Transfascial suture fixation technique in laparoscopic repair of inguinal hernia
Authors: Chan Shun‐Yan B 
Published: May 2019

AbstractIntroductionThis study presents the initial results of a transfascial suture mesh fixation technique. This method was devised to reduce operative costs and foreign body‐associated risks while embracing the benefits of fixation in laparoscopic inguinal hernia repair.Materials and Surgical TechniquePatients undergoing laparoscopic inguinal hernia repair with transfascial suture fixation (TRANSFIX) in our center between March 2017 and March 2018 were retrospectively reviewed. The procedure is orchestrated by a reusable fascial closure device sequentially puncturing the fascia vertically through the inferior port site and guiding a polypropylene thread through the mesh. The thread is retrieved from the extraperitoneal plane with the device, creating an extracorporeal suture loop to embed a surgical knot at the subcutaneous layer of the port site.DiscussionIn its first year after introduction, 16 TRANSFIX were performed. All patients were men (mean age, 62.6 years). Thirteen hernias (81.3%) were first occurrence, and three (18.8%) were recurrent. Twelve (75.0%) were direct hernias, and three (18.8%) were indirect hernias; one patient presented with concurrent direct and indirect hernia. Median operating time was 41.5 minutes for unilateral repair and 73.0 minutes for bilateral. Median blood loss was 5 mL. One patient had a seroma after unilateral indirect hernia repair. After a median follow‐up of 15.5 months (range, 9‐21 months), no patient had chronic pain, wound infection, hematoma, or recurrence. Instrumental cost reduction per operation was between $150 and $300. TRANSFIX appears to be a safe and economical mesh fixation method.
The Production Effect Improves Memory in 7‐ to 10‐Year‐Old Children
Authors: Pritchard Verena E. , Heron‐Delaney Michelle , Malone Stephanie A. , MacLeod Colin M. 
Published: May 2019

The production effect—whereby reading words aloud improves memory for those words relative to reading them silently—was investigated in two experiments with 7‐ to 10‐year‐old children residing in Brisbane, Australia. Experiment 1 (n = 41) involved familiar printed words, with words read aloud or silently appearing either in mixed‐ or blocked‐list formats in a within‐subject design. Recognition for words read aloud was better than for those read silently, an effect consistent across both list formats. These results were confirmed in Experiment 2 (n = 40) using longer lists of printed novel nonwords. Final analyses indicated that the production effect was comparable for words and nonwords. Findings are discussed in relation to the distinctiveness account and the use of production as a mnemonic in children.