bluuebunny/crossref_metadata_2025 huggingface dataset:
Secularism and Religion
Authors: Kettell Steven
Published: February 2019

The boundary between the religious and the secular spheres of life is contested in many parts of the world. From the latter decades of the 20th century, controversies over issues such as the legalization of same-sex marriage, assisted dying, and freedom of speech, as well as clashes around reproductive rights and equality issues, have all featured highly on national political agendas. Set against a backdrop of the “return of religion” to public life, these debates and tensions have given rise to the notion that secularism might be in a state of crisis or moving toward some form of post-secular condition. The term “secularism” is itself also contested. The precise nature of the “secular” and the “religious” spheres of life is subject to interpretation, and secularism in practice can be manifest in a number of ways. This ranges from exclusivist forms of secularism in countries such as the United States and France to inclusive secularism in the case of India. Supporters of a role for religion in public life maintain that religion provides a range of valuable public goods and gives individuals a sense of meaning and identity. Secularists, on the other hand, claim that the separation of church and state provides the best framework for upholding the rights and freedoms of all citizens regardless of their religion or belief.
Physical Contexts and Behavioral Aging
Authors: Oswald Frank , Wahl Hans-Werner
Published: February 2019

Along with the social, economic, care-related, organizational, and technological context, the physical and infrastructural environment indoors and out of the home has gained attention in behavioral aging research as well as in gerontology as a whole since the 1960s. There is, however, an ongoing trend to downplay physical-infrastructural environments in behavioral aging research at the conceptual and empirical level. Therefore, substance is provided to support the usefulness of ecology and aging perspectives for the psychology of aging by mainly addressing North American and European research in the area.
Family Systems Therapy
Authors: Qualls Sara Honn , Edwards Lacey
Published: February 2019

Family systems therapy seeks to alter the structure or processes of a family for the purposes of reducing distress in one or more persons and improving the ability of the family to meet members’ needs. Building from a general systems paradigm, family systems therapy recognizes that family structures shift over time as they respond to members’ developmental processes and broader system demands. As members enter and exit or change capacity, and as external stressors arise, the family typically uses adaptive processes to demonstrate resilience. Family systems therapy is useful when the family struggles to adapt, or the adaptation strategy further stresses the family.

Multiple models of family systems therapies offer variations in intervention approaches but have common tenets. Major models include Ackerman’s early psychodynamics model, transgenerational models of family therapy, structural family therapy, strategic family therapy, and communications approaches to family therapy. Models vary in their recommended roles for the therapist, strategies for therapist and family, and the salience of immediate versus longer-term goals. Family systems therapies conceptualize family interactions as complex, reciprocal, open, self-organizing, adaptive, social constructionist, and meaning-making.

Family systems therapy also can be used with systems larger than families, such as schools or organizations, or to understand cultural phenomena. The field of marriage and family therapy has defined competencies for practice, training requirements, and licensure standards and established national and international professional organizations.
International Perspectives on Residential Aged Care
Authors: Sadeq Nasreen A. , Molinari Victor
Published: February 2019

The need for facilities that provide residential aged care is expected to increase significantly in the near future as the global population ages at an unprecedented rate. Many older adults will need to be placed in a residential care setting, such as an assisted living facility (ALF) or nursing home, when their caregivers can no longer effectively manage serious medical or psychiatric conditions at home. Although the types of residential care settings worldwide vary considerably, long-term care residents (LTC) and staff benefit from environmental and cultural changes in LTC settings. Unlike traditional medical models of LTC, culture change advocates for a shift toward holistic, person-centered care that takes place in homelike environments and accounts for the psychosocial needs of residents. Carving out a role for family members and training professional caregivers to address behavioral problems and quality-of-life issues remain a challenge. In LTC settings, preliminary research indicates that implementing person-centered changes addressing resident and caregiver needs may lead to better health outcomes, as well as increased satisfaction among patients, families, and staff. With the burgeoning world population of older adults, it is incumbent that they be provided with optimal humane culturally sensitive care.
Place Managers and Crime Places
Authors: Eck John E.
Published: February 2019

Place management theory—a part of routine activity theory—explains why a relatively few places have a great deal of crime while most places have little or no crime. The explanation is the way place managers carry out their four primary functions: organization of space, regulation of conduct, control of access, and acquisition of resources.

Place managers are those people and organizations that own and operate businesses, homes, hotels, drinking establishments, schools, government offices, places of worship, health centers, and other specific locations. They can even operate mobile places such as busses, trains, ships, and aircraft. Some are large—a multi-story office tower for example—while others are tiny—a bus stop, for example. Place managers are important because they can exercise control over the people who use these locations and in doing so contribute to public order and safety. Consequently, it is important to understand place management, how it can fail, and what one can do to prevent failures.

Place management has implications beyond high-crime sites. When crime places are connected, they can create crime hot spots in an area. The concentration of high crime places can inflate crime in a neighborhood. Moreover, place management can be applied to virtual locations, such as servers, websites, and other network infrastructures.

There is considerable evaluation evidence that place managers can change high crime locations to low crime locations. Research also shows that displacement to other places, though possible, is far from inevitable. Indeed, research shows that improving a high crime place can reduce crime at places nearby places. Although much of this research has studied how police intervene with place managers, non-police regulatory agencies can carry out this public safety function.
Arts and Peacebuilding
Authors: Hunter Mary Ann , Cohen Cynthia E.
Published: February 2019

The arts have long been associated with social transformation and peacebuilding. In conflict-affected settings, the arts can serve to raise awareness of the impacts of violence, enable distinctive expressions of culture, offer opportunities for intercultural collaboration, and embody affective and aesthetic means of engaging with trauma and healing. Conversely, the arts also have the potential to harm, when they are used in the name of propaganda, for example, or result in re-traumatizing victims of conflict in an aestheticization of experience. An emerging interdisciplinary field of arts and peacebuilding is researching the arts’ potential to restore capacities that might have been eclipsed by violence and long-standing oppression—that is, arts practice at the nexus of reconciliation, community development, and social justice. As the field grows, scholarship in peace studies, applied arts, conflict resolution, and peace education is contributing to a productive troubling of definitions of peace and is drawing attention to the role of affect, cultural diversity, and coloniality in such work. Future scholarship in which the arts are conceptualized beyond the instrumental benefits to their multiple legitimate purposes as a “way of knowing” will more appropriately capture the complexities, uncertainties, and paradoxes of imagining and building peace through the arts in diverse contexts. Key international projects continue to decolonize universalizing definitions and practices of the arts by documenting and investigating a range of aesthetic practices in peacebuilding. This work is being generated and disseminated broadly across disciplinary scholarly communities, government and nongovernment agencies, and professional networks of educators and artists. The nexus of arts and peacebuilding theory has much to offer the mobilization of new directions in peacebuilding practice and an integration of arts-based peace education.
Women and Reproduction in the United States during the 19th Century
Authors: Withycombe Shannon K.
Published: February 2019

Throughout the 19th century, American women experienced vast changes regarding possibilities for childbirth and for enhancing or restricting fertility control. At the beginning of the century, issues involving reproduction were discussed primarily in domestic, private settings among women’s networks that included family members, neighbors, or midwives. In the face of massive social and economic changes due to industrialization, urbanization, and immigration, many working-class women became separated from these traditional networks and knowledge and found themselves reliant upon emerging medical systems for care and advice during pregnancy and childbirth. At the same time, upper-class women sought out men in the emerging profession of obstetrics to deliver their babies in hopes of beating the frightening odds against maternal and infant health and even survival. Nineteenth-century reproduction was altered drastically with the printing and commercial boom of the middle of the century. Families could now access contraception and abortion methods and information, which was available earlier in the century albeit in a more private and limited manner, through newspapers, popular books, stores, and from door-to-door salesmen. As fertility control entered these public spaces, many policy makers became concerned about the impacts of such practices on the character and future of the nation. By the 1880s, contraception and abortion came under legal restrictions, just as women and their partners gained access to safer and more effective products than ever before. When the 19th century closed, legislatures and the medical profession raised obstacles that hindered the ability of most women to limit the size of their families as the national fertility rate reached an all-time low. Clearly, American families eagerly seized opportunities to exercise control over their reproductive destinies and their lives.
The Knights of Labor
Authors: Hild Matthew
Published: February 2019

Founded in Philadelphia in 1869, the Noble and Holy Order of the Knights of Labor became the largest and most powerful labor organization that had ever existed in the United States by the mid-1880s. Recruiting men and women of nearly all occupations and all races (except Chinese), the Knights tried to reform American capitalism and politics in ways that would curb the growing economic and political abuses and excesses of the Gilded Age. Leaders of the organization viewed strikes as harmful to workers and employers alike, especially after the Great Railroad Strike of 1877, but a series of railroad strikes in 1884 and 1885 caused the Knights’ membership rolls to reach a peak of at least 700,000 in 1886.

The heyday of the Knights of Labor proved brief though. Two major events in May 1886, the Haymarket riot in Chicago and the failure of a strike against Jay Gould’s Southwestern Railway system, began a series of setbacks that caused the organization to decline about as rapidly as it had arisen. By 1893, membership dropped below 100,000, and the Knights’ leaders aligned the organization with the farmers’ movement and the Populist Party. The Knights increasingly became a rural organization, as urban skilled and semi-skilled workers joined trade unions affiliated with the American Federation of Labor (AFL). The AFL, however, proved less inclusive and egalitarian than the Knights of Labor, although some of the latter’s ideals would be carried on by later organizations such as the Industrial Workers of the World and the Congress of Industrial Organizations.
Nondipping Pattern and Cardiovascular and Renal Damage in a Population-Based Study (The STANISLAS Cohort Study)
Authors: Lopez-Sublet Marilucy , Girerd Nicolas , Bozec Erwan , Machu Jean-Loup , Ferreira João Pedro , Zannad Faiez , Mourad Jean-Jacques , Rossignol Patrick
Published: February 2019

OBJECTIVE

The attenuation of physiological nocturnal decline of blood pressure (BP)—called nondipper pattern—has previously been reported to be associated with target organ damage in hypertensive subjects. However, this association remains debated and poorly studied in normotensive patients. This study aimed to investigate the association between nondipper pattern and subclinical cardiovascular and renal damage in an initially healthy population-based cohort study.

METHODS

The STANISLAS Cohort is a single-center, familial longitudinal cohort composed of 1,006 families (4,295 subjects) recruited in 1993–1995 for a 5-year periodic health examination. A total of 1,334 subjects from the 4th visit (2011–2016) of the STANISLAS cohort were included. This 4th examination included estimated glomerular filtration rate, albumin/creatinine ratio, pulse wave velocity, central systolic BP, carotid intima–media thickness and distensibility, left ventricular mass index, left ventricular hypertrophy, diastolic dysfunction, and ambulatory blood pressure monitoring (ABPM). Nondipping status was defined as a mean reduction in systolic BP (SBP) or diastolic BP (DBP) lower than 10% during nighttime.

RESULTS

Data were obtained from 798 normotensive subjects (45 ± 14 years, 395 [49%] nondippers, SBP/DBP mmHg 24 hours: 116/71 ± 7/5) and 536 hypertensive patients (56 ± 11 years, 257 [48%] nondippers, SBP/DBP mmHg 24 hours: 127/78 ± 10/7). Mean 24-hour and daytime ABPM measurements were within the normal range, even in hypertensive participants (19% treated). The nondipping pattern was not associated with cardiovascular or renal alterations in this population.

CONCLUSION

In this middle-aged population with an overall 24-hour optimal BP control, the nondipper pattern was not associated with increased cardiovascular or renal damage.
Assembly Graph Browser: interactive visualization of assembly graphs
Authors: Mikheenko Alla , Kolmogorov Mikhail
Published: February 2019

Currently, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that provide a more comprehensive representation of an assembly. Since interactive visualization of large assembly graphs remains an open problem, we developed an Assembly Graph Browser (AGB) tool that visualizes large assembly graphs, extending the functionality of previously developed visualization approaches. Assembly Graph Browser includes a number of novel functions including repeat analysis, construction of the contracted assembly graphs (i.e. the graphs obtained by collapsing a selected set of edges) and a new approach to visualizing large assembly graphs.

Availability and implementation

http://www.github.com/almiheenko/AGB.

Supplementary information

Supplementary data are available at Bioinformatics online.
SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution
Authors: Kundu Soumya , Bansal Mukul S
Published: February 2019

SaGePhy is a software package for improved phylogenetic simulation of gene and subgene evolution. SaGePhy can be used to generate species trees, gene trees and subgene or (protein) domain trees using a probabilistic birth–death process that allows for gene and subgene duplication, horizontal gene and subgene transfer and gene and subgene loss. SaGePhy implements a range of important features not found in other phylogenetic simulation frameworks/software. These include (i) simulation of subgene or domain level evolution inside one or more gene trees, (ii) simultaneous simulation of both additive and replacing horizontal gene/subgene transfers and (iii) probabilistic sampling of species tree and gene tree nodes, respectively, for gene- and domain-family birth. SaGePhy is open-source, platform independent and written in Java and Python.

Availability and implementation

Executables, source code (open-source under the revised BSD license) and a detailed manual are freely available from http://compbio.engr.uconn.edu/software/sagephy/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Rifampicin effect on intracellular and plasma pharmacokinetics of tenofovir alafenamide
Authors: Cerrone Maddalena , Alfarisi Omamah , Neary Megan , Marzinke Mark A , Parsons Teresa L , Owen Andrew , Maartens Gary , Pozniak Anton , Flexner Charles , Boffito Marta
Published: February 2019

Objectives

Tenofovir alafenamide produces lower plasma tenofovir and higher intracellular tenofovir diphosphate (DP) concentrations than tenofovir disoproxil fumarate but it is likely a victim of interactions with rifampicin. We aimed to investigate the pharmacokinetics of tenofovir alafenamide/emtricitabine with rifampicin.

Patients and methods

Healthy volunteers received tenofovir alafenamide/emtricitabine at 25/200 mg once daily, followed by tenofovir alafenamide/emtricitabine + rifampicin daily followed by tenofovir disoproxil fumarate. Plasma tenofovir alafenamide, tenofovir, emtricitabine and intracellular tenofovir-DP and emtricitabine triphosphate pharmacokinetics and genetic polymorphisms were assessed.

Results

Tenofovir alafenamide exposure decreased when tenofovir alafenamide/emtricitabine + rifampicin was used compared with tenofovir alafenamide/emtricitabine [geometric mean ratio (GMR) (90% CI): 0.45 (0.33–0.60)]. Plasma tenofovir and intracellular tenofovir-DP concentrations decreased with rifampicin [GMR (90% CI): 0.46 (0.40–0.52) and 0.64 (0.54–0.75), respectively]. GMR (90% CI) of intracellular tenofovir-DP AUC0–24 for tenofovir alafenamide/emtricitabine + rifampicin versus tenofovir disoproxil fumarate was 4.21 (2.98–5.95). Rifampicin did not affect emtricitabine pharmacokinetics. CYP3A4*22 rs35599367 was associated with higher plasma tenofovir alafenamide AUC0–24 at day 56.

Conclusions

Following tenofovir alafenamide/emtricitabine administration with rifampicin, intracellular tenofovir-DP concentrations were still 4.21-fold higher than those achieved by tenofovir disoproxil fumarate, supporting further study during HIV/TB co-infection.
The Clinical Value of Heart Rate Monitoring Using an Apple Watch
Authors: Karmen Carol L. , Reisfeld Michael A. , McIntyre Matthew K. , Timmermans Robert , Frishman William
Published: February 2019

Public interest in health monitoring devices has increased with the availability of wearable technologies or wearables such as the Apple Watch. These devices are collecting health data that may be useful to health professionals. Most studies to date have been conducted with a limited sample size and with healthy subjects. Recent studies have suggested the usefulness of long-term cardiac monitoring to reveal atrial fibrillation and prevent cryptogenic stroke. Wearable devices may become useful in cardiac monitoring, and further studies are needed.
Influence of Severity on Aesthetic Outcomes of Unilateral Cleft Lip Repair in 1,823 Patients
Authors: Campbell Alex , Restrepo Carolina , Park Eugene , Navas Genesis , Deshpande Gaurav , Swanson Jordan , Schonmeyr Bjorn , Wendby Lisa , Ayala Ruben
Published: February 2019

Background:

Although efforts to improve access to care for patients with cleft lip in the developing world have grown tremendously, there is a dearth of data regarding aesthetic outcomes after cleft lip repairs in this setting. Defining severity-outcome relationships has the potential to improve efficiency of care delivery in resource-limited settings, and to improve overall results. In this study, we investigate the relationship between initial cleft lip severity and early aesthetic outcomes following surgical repair of primary unilateral cleft lip.

Methods:

Using previously validated tools to assess unilateral cleft lip severity and aesthetic outcome after repair, we evaluated 1,823 consecutive patients who underwent primary unilateral cleft lip/nose (UCL/N) repair. Three separate evaluators scored each case for a total of 5,469 total independent evaluations.

Results:

Our results show that with increasing severity of UCL/N deformity, there is a corresponding decrease in early aesthetic outcome scores. Using our results, we established normative early aesthetic outcomes following repair for each severity grade of UCL/N deformity.

Conclusions:

In conclusion, this study has achieved a standardized, timely, and cost-effective evaluation of 1,823 surgical cases of primary UCL/N repair. This data set provides a normal distribution of aesthetic results according to initial cleft severity and defines a standard of “expected” aesthetic results after primary UCL/N repair. Our results also show a clear correlation between initial severity and immediate aesthetic result after surgery, though we also show that excellent results are possible regardless of initial cleft severity.
Recent Advances in Antiemetics
Authors: Smith Carrie , Smith Michele , Cunningham Regina , Davis Susan
Published: February 2019

Background:

Despite the availability of effective antiemetic regimens, patients still experience chemotherapy-induced nausea and vomiting (CINV). 5-Hydroxytryptamine 3 (5-HT3) receptor antagonists (RAs) are the mainstay of CINV prevention, and updated antiemetic guidelines include new options.

Objective:

The aim of this study was to highlight advances in CINV management, focusing on new 5-HT3 RA formulations in adults, updated antiemetic guidelines, and the role of nurses.

Methods:

MEDLINE searches were conducted for English-language publications for the past 15 years using relevant search terms (“serotonin receptor antagonist,” “5-HT3 receptor antagonist,” “antiemetic,” “chemotherapy-induced nausea and vomiting”) in the abstract or title. Abstracts at relevant major congresses for the past 3 years and additional pivotal publications were included. The most informative, relevant, and current publications were included.

Results:

5-Hydroxytryptamine 3 RAs are effective in preventing acute (0–24 hours) CINV but less effective in the delayed phase (24–120 hours) given their short half-lives. Updated antiemetic guidelines include fixed-dose intravenous fosnetupitant and palonosetron (IV NEPA) and granisetron extended-release subcutaneous injection, a recently approved 5-HT3 RA formulation providing slow, controlled release of therapeutic granisetron concentrations for 5 days or longer. Nurses play a pivotal role in implementing updated guideline-recommended antiemetic regimens for highly and some moderately emetogenic chemotherapy regimens, comprising a 4- or 3-drug regimen of 5-HT3 RA, neurokinin-1 RA, and dexamethasone, with/without olanzapine.

Conclusion:

Newer antiemetic combinations and formulations provide flexibility for CINV prevention. Granisetron extended-release subcutaneous injection is a convenient subcutaneous granisetron option.

Implications for Practice:

Nurses play a critical role in understanding and using new antiemetic formulations and updated antiemetic guidelines in their practices.
Oea Signaling Pathways and the Metabolic Benefits of Vertical Sleeve Gastrectomy
Authors: Hutch Chelsea R. , Trakimas Danielle R. , Roelofs Karen , Pressler Joshua , Sorrell Joyce , Cota Daniela , Obici Silvana , Sandoval Darleen A.
Published: February 2019

Objective:

The aim of this study was to determine whether downstream [peroxisome proliferator-activated-receptor alpha (PPARα) and the G-protein coupled receptor, GPR119] and upstream (a fatty acid translocase, CD36) signaling targets of N-oleoylethanolamide (OEA) were necessary for weight loss, metabolic improvements, and diet preference following vertical sleeve gastrectomy (VSG).

Summary Background Data:

OEA is an anorectic N-acylethanolamine produced from dietary fats within the intestinal lumen that can modulate lipid metabolism, insulin secretion, and energy expenditure by activating targets such as PPARα and GPR119.

Methods:

Diet-induced obese mice, including wild-type or whole body knockout (KO) of PPARα, GPR119, and CD36, were stratified to either VSG or sham surgery before body weight, body composition, diet preference, and glucose and lipid metabolic endpoints were assessed.

Results:

We found increased duodenal production of OEA and expression of both GPR119 and CD36 were upregulated in wild-type mice after VSG. However, weight loss and glucose tolerance were improved in response to VSG in PPARαKO, GPR119KO, and CD36KO mice. In fact, VSG corrected hepatic triglyceride dysregulation in CD36KO mice, and circulating triglyceride and cholesterol levels in PPARαKO mice. Lastly, we found PPARα-mediated signaling contributes to macronutrient preference independent of VSG, while removal of CD36 signaling blunts the VSG-induced shift toward carbohydrate preference.

Conclusions:

In the search for more effective and less invasive therapies to help reverse the global acceleration of obesity and obesity-related disease OEA is a promising candidate; however, our data indicate that it is not an underlying mechanism of the effectiveness of VSG.
High Calcineurin Inhibitor Intrapatient Variability Is Associated With Renal Allograft Inflammation, Chronicity, and Graft Loss
Authors: Sharma Akhil , Cherukuri Aravind , Mehta Rajil B. , Sood Puneet , Hariharan Sundaram
Published: February 2019

Background

High calcineurin inhibitor (CNI) intrapatient variability (IPV) has been associated with poor kidney allograft outcomes. However, the relationship between early allograft histological changes, their progression, and CNI-IPV is less well studied. Hence, we evaluated effect of CNI-IPV defined by the degree of fluctuation of CNI levels in all kidney transplant patients over 2 to 12 months posttransplant on early allograft inflammation, subsequent chronicity, and later clinical outcomes.

Methods

Two hundred eighty-six patients transplanted from January 2013 to November 2014 were enrolled with protocol and indication biopsies. The mean CNI-IPV was 28.5% and a quarter of our cohort had IPV of 35% or greater (high CNI IPV). Baseline demographic differences were similar between high and low CNI IPV groups.

Results

High CNI-IPV was associated with a higher incidence of acute rejection (AR) within 1 year (52% vs 31% P < 0.001), more persistent/recurrent AR by 1 year (18.2% vs 6.2%, P = 0.002), higher-grade AR (≥Banff 1B, 27.5% vs 7.3%, P < 0.001), and worse interstitial fibrosis/tubular atrophy (P = 0.005). High CNI-IPV was associated with increased graft loss (GL) and impending graft loss (iGL, defined as eGFR<30 ml/min and >30% decline in eGFR from baseline), regardless of donor-specific antibody, delayed graft function, rejection, or race. In a multivariate Cox Proportional Hazards Model, high CNI-IPV was independently associated with GL + iGL (hazard ratio, 3.1; 95% confidence interval, 1.6–5.9, P < 0.001).

Conclusions

High CNI-IPV within 1 year posttransplant is associated with higher incidence of AR, severe AR, allograft chronicity, GL, and iGL. This represents a subset of patients who are at risk for poor kidney transplant outcomes and potentially a modifiable risk factor for late allograft loss.
Reconstruction of a Pancreatic Allograft With Variant Arterial Anatomy for Transplantation
Authors: Adamson Dylan , Holzner Matthew L. , Wadhera Vikram , Shapiro Ron
Published: February 2019

Donor pancreas utilization rates remain low and aberrant donor anatomy can lead to organ discard by transplant centers. We report on a case of successful pancreas transplantation using a graft with variant arterial anatomy demonstrating that arterial reconstruction is a viable option if aberrant anatomy is encountered at the donor operation. Efforts must be made to use all pancreas grafts that are felt to be of appropriate quality.
Maternal Protection in Childhood is Associated with Amygdala Reactivity and Structural Connectivity in Adulthood
Authors: Farber Madeline J. , Kim M. Justin , Knodt Annchen R. , Hariri Ahmad R.
Published: February 2019

Recently, we reported that variability in early-life caregiving experiences maps onto individual differences in threat-related brain function. Specifically, we found that greater familial affective responsiveness is associated with increased amygdala reactivity to interpersonal threat, particularly in adolescents having experienced relatively low recent stress. Here, we conceptually replicate and extend on our previous work to provide further evidence that subtle variability in specific features of early caregiving shapes structural and functional connectivity between the amygdala and medial prefrontal cortex (mPFC) in a cohort of 312 young adult volunteers. Multiple regression analyses revealed that participants who reported higher maternal but not paternal protection exhibited increased amygdala reactivity to explicit signals of interpersonal threat (i.e., angry facial expressions) but not implicit signals of broad environmental threat (i.e., fearful facial expressions). While amygdala functional connectivity with regulatory regions of the mPFC was not significantly associated with maternal protection, participants who reported higher maternal protection exhibited relatively decreased structural integrity of the uncinate fasciculus (UF), a white matter tract connecting these same brain regions. The observed associations were independent of the potential confounding influences of participant sex, socioeconomic status, and self-reported childhood trauma. There were no significant associations between structural or functional brain measures and either maternal or paternal care ratings. These findings suggest that an over controlling parenting style in mothers during childhood is associated with functional and structural alterations of brain regions involved in generating and regulating responses to threat in young adulthood.
Addressing reverse inference in structural brain alterations
Authors: Cauda Franco , Nani Andrea , Liloia Donato , Manuello Jordi , Premi Enrico , Duca Sergio , Fox Peter T. , Costa Tommaso
Published: February 2019

In neuroimaging with reverse inferences we can infer the involvement of cognitive processes from certain patterns of brain activity. Still, the same reasoning holds if we substitute “brain activity” with “brain alteration” and “cognitive process” with “brain disorder”. To assess the involvement of a certain alteration pattern in a brain disorder we used the Bayes’ factor technique on voxel-based morphometry data of schizophrenia and Alzheimer’s disease. This technique allows to calculate the ratio between the likelihoods of two alternative hypotheses (in our case, that the alteration of the voxel is specific for the brain disorder under scrutiny or that the alteration is not specific). We then performed temporal simulations of the alteration spread associated with different pathologies. The Bayes’ factor values calculated on these simulated data were able to reveal that the areas which are more specific to a certain disease are also the ones to be early altered.
Coordinate-based mapping of tabular data enables fast and scalable queries
Authors: Piccolo Stephen R. , Ence Zachary E. , Hill Kimball , Tatlow PJ , Fry Brandon J. , Dayton Jonathan B.
Published: February 2019

Motivation

Biologists commonly store data in tabular form with observations as rows, attributes as columns, and measurements as values. Due to advances in high-throughput technologies, the sizes of tabular datasets are increasing. Some datasets contain millions of rows or columns. To work effectively with such data, researchers must be able to efficiently extract subsets of the data (using filters to select specific rows and retrieving specific columns). However, existing methodologies for querying tabular data do not scale adequately to large datasets or require specialized tools for processing. We sought a methodology that would overcome these challenges and that could be applied to an existing, text-based format.

Results

In a systematic benchmark, we tested 10 techniques for querying simulated, tabular datasets. These techniques included a delimiter-splitting method, the Pythonpandasmodule, regular expressions, object serialization, theawkutility, and string-based indexing. We found that storing the data in fixed-width formats provided excellent performance for extracting data subsets. Because columns have the same width on every row, we could pre-calculate column and row coordinates and quickly extract relevant data from the files. Memory mapping led to additional performance gains. A limitation of fixed-width files is the increased storage requirement of buffer characters. Compression algorithms help to mitigate this limitation at a cost of reduced query speeds. Lastly, we used this methodology to transpose tabular files that were hundreds of gigabytes in size, without creating temporary files. We propose coordinate-based, fixed-width storage as a fast, scalable methodology for querying tabular biological data.

Contact

stephen_piccolo@byu.edu
A novel QTL conferring Fusarium crown rot resistance located on chromosome arm 6HL in barley
Authors: Gao Shang , Zheng Zhi , Hu Haiyan , Shi Haoran , Ma Jian , Liu Yaxi , Wei Yuming , Zheng You-Liang , Zhou Meixue , Liu Chunji
Published: February 2019

Fusarium crown rot (FCR), caused primarily by Fusarium pseudograminearum, is a devastating disease for cereal production in semi-arid regions worldwide. To identify and characterize loci conferring FCR resistance, we assessed a landrace AWCS799 which is among the top lines identified from a screening. Genetic control of its resistance was investigated by generating and analysing two populations of recombinant inbred lines. One of the populations was used for QTL detection and the other for validation. A novel QTL, located on the long arm of chromosome 6H (designated as Qcrs.caf-6H), was consistently detected in each of the four trials conducted against the mapping population. The QTL explained up to 29.1% of the phenotypic variance and its effect was confirmed in the validation population. Significant interactions between this resistance locus and either plant height or heading date were not detected, further facilitating its manipulation in breeding programs.

Key Message

This study identified and validated a novel and large-effect QTL conferring Fusarium crown rot resistance on the long arm of chromosome 6HL in barley.
Antibiotic Treatment Drives the Diversification of the Human Gut Resistome
Authors: Li Jun , Rettedal Elizabeth A. , van der Helm Eric , Ellabaan Mostafa , Panagiotou Gianni , Sommer Morten O.A.
Published: February 2019

Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.
Saffron (Crocus sativus) is an autotriploid that evolved in Attica (Greece) from wildCrocus cartwrightianus
Authors: Nemati Zahra , Harpke Dörte , Gemicioglu Almila , Kerndorff Helmut , Blattner Frank R.
Published: February 2019

Crocus sativusis the source of saffron, which is made from dried stigmas of the plant. It is a male-sterile triploid that ever since its origin has been propagated vegetatively. The mode of evolution and area of origin of saffron are matters of long-lasting debates. Here we analyzed chloroplast genomes, genotyping-by-sequencing (GBS) data, nuclear single-copy genes, and genome sizes to solve these controversial issues. We could place 99.3% of saffron GBS alleles inCrocus cartwrightianus, a species occurring in southern mainland Greece and on Aegean islands, identifying it as the sole progenitor of saffron. Phylogenetic and population assignment analyses together with chloroplast polymorphisms indicated the wildC. cartwrightianuspopulation south of Athens as most similar toC. sativus. We conclude that the crop is an autotriploid that evolved in Attica by combining two different genotypes ofC. cartwrightianus. Vegetative propagation prevented afterwards segregation of the favorable traits of saffron.
Pannexin-1 Channels govern the Generation of Necroptotic small Extracellular Vesicles
Authors: Douanne Tiphaine , André-Grégoire Gwennan , Feyeux Magalie , Hulin Philippe , Gavard Julie , Bidère Nicolas
Published: February 2019

The activation of mixed lineage kinase-like (MLKL) by receptor-interacting protein kinase-3 (RIPK3) controls the execution of necroptosis, a regulated form of necrosis that occurs in apoptosis-deficient conditions. Active oligomerized MLKL triggers the exposure of phosphatidylserine residues on the cell surface and disrupts the plasma membrane integrity by forming lytic pores. MLKL also governs the biogenesis and shedding of proinflammatory small extracellular vesicles (EVs) during the early steps of necroptosis, however the molecular basis is unknown. Here, we find that MLKL oligomers activate plasma membrane Pannexin-1 (PANX1) channels, concomitantly to the loss of phosphatidylserine asymmetry. This plasma membrane “leakiness” requires the Rab GTPase Rab27 isoforms, which usher the small EVs to their release. Conversely, PANX1 knockdown disorganized the small EVs machinery and precludes vesicles extrusion. These data identify a novel signaling nexus between MLKL, Rab27, and PANX1, and propose ways to interfere with small EV generation.
The coiled coil domain of DEF6 facilitates formation of large vesicle-like, cytoplasmic aggregates that trap the P-body marker DCP1 and exhibit prion-like features
Authors: Cheng Huaitao , Sablitzky Fred
Published: February 2019

DEF6, also known as SLAT and IBP, is critical for the development of autoimmune disease and cancer. In T cells, DEF6 participates in TCR-mediated signalling determining T helper cell-mediated immune responses. In addition, DEF6 acts as a guanine nucleotide exchange factor for Rho GTPases facilitating F-actin assembly and stabilisation of the immunological synapse. However, DEF6 is also a component of mRNA processing bodies (P-bodies) linking it to mRNA metabolism. DEF6 can adopt multiple conformations that result in different cellular localisations and functions. Post translational modifications such as phosphorylation result in conformational change liberating functional domains that are masked in the native stage of DEF6. ITK phosphorylation of Try210/222 liberates the N-terminal end and to a certain extend also the C-terminal coiled coil domain of DEF6 resulting in P-body colocalisation. In fact, the N-terminal 45 amino acids of DEF6 that encode a Ca2+-binding EF hand are sufficient to target P-bodies. Mutant proteins that unleashed the C-terminal coiled coil domain of DEF6 spontaneously aggregated forming large vesicle-like, cytoplasmic structures. These aggregates trapped proteins such as the P-body component DCP1 altering its cytoplasmic localisation. However, cellular stress reversed aggregate formation in mutant DEF6 proteins that contained ITAM and PH domain in conjunction with the coiled coil domain resulting in colocalisation with DCP1. Furthermore, coiled coil-mediated aggregates appeared to function like prions enforcing conformational change onto wild type DEF6 protein.
Short-term gain, long-term pain: the senescence life cycle and cancer
Authors: Chan Adelyne Sue Li , Narita Masashi
Published: February 2019

Originally thought of as a stress response end point, the view of cellular senescence has since evolved into one encompassing a wide range of physiological and pathological functions, including both protumorignic and antitumorigenic features. It has also become evident that senescence is a highly dynamic and heterogenous process. Efforts to reconcile the beneficial and detrimental features of senescence suggest that physiological functions require the transient presence of senescent cells in the tissue microenvironment. Here, we propose the concept of a physiological “senescence life cycle,” which has pathological consequences if not executed in its entirety.
A Retrospective Study of Intentional Body Dismemberment in New York City: 1996–2017
Authors: Adams Bradley J. , Rainwater Christopher W. , Yim An‐Di , Alesbury Helen S.
Published: February 2019

A review of New York City dismemberment cases occurring between 1996 and 2017 was conducted, which resulted in a total of 55 dismembered decedents in a 22‐year period. Annual trends indicate an average of 2.5 dismembered decedents. Additional results show that 53% of cases involved transection only, 35% involved disarticulation only, and 13% involved a combination of both. When the entire body could be accounted for, the average number of body portions per case was 5.5. Frequent locations for dismemberment were the neck, shoulders, hips, and knees. Dismemberment locations showed a general trend of anatomical symmetry. Seventy‐eight percent of the dismemberments involve disposal of body parts in an outside location. Eighty‐four percent were concealed from view with some type of covering. The findings from New York City are compared with other studies.
Pits, mounds, and vernal ponds in a Tasmanian subalpine grassland
Authors: Harrison‐Day Violet , Kirkpatrick James
Published: February 2019

Falling trees commonly turbate soils in primary forest, creating characteristic edaphic patterns related to pit and mound topography. Vernal ponds with associated mounds were observed in mineral soils on a treeless plain in subalpine Tasmania, Australia. The hypothesis that paired ponds and mounds on the plain originated as pit and mound features in forests that were later destroyed by fire was tested by comparing the soils and landforms caused by recent tree falls in adjacent forest with those on the plain. The soil characteristics, orientations, and dimensions of the ponds and mounds were consistent with a tree fall origin, although rare secondary ponds on the tops of mounds may derive from the burrowing activities of the medium‐sized marsupial, Vombatus ursinus (common wombat). The characteristics of pond and mound soils suggested that most were hundreds to thousands of years old, with the ponds persisting because of differences in deflation, deposition, and organic matter formation between themselves and adjacent persistently dry land.
Role of gut microbial metabolites in nonalcoholic fatty liver disease
Authors: Zhao Ze Hua , Lai Jonathan King‐Lam , Qiao Liang , Fan Jian Gao
Published: February 2019

Nonalcoholic fatty liver disease (NAFLD) is a common, multifactorial liver disease that has emerged as a global challenge due to its increasing prevalence and lack of sustainable treatment options. Gut microbiota possess vital functions in fermenting dietary nutrients and synthesizing bioactive molecules. This function is of great importance in maintaining health because these microbial metabolites are essential in regulating energy metabolism, immune response, and other vital physiological processes. Altered gut flora can result in a change in gut microbial metabolites, affecting the onset and progression of multiple diseases. In this review we summarize the metabolites that may have beneficial or harmful effects on the development and progression of NAFLD. This will help us better understand the possible mechanisms underlying the pathogenesis of NAFLD and facilitate the identification of potential therapeutic approaches for NAFLD.
A Population‐wide study of electrocardiographic (ECG) norms and the effect of demographic and anthropometric factors on selected ECG characteristics in young, Southeast Asian males—results from the Singapore Armed Forces ECG (SAFE) study
Authors: Sia Ching‐Hui , Dalakoti Mayank , Tan Benjamin Y. Q. , Lee Edward C. Y. , Shen Xiayan , Wang Kangjie , Lee Joshua S. , Arulanandam Shalini , Chow Weien , Yeo Tee Joo , Yeo Khung Keong , Chua Terrance S. J. , Tan Ru San , Lam Carolyn S. P. , Chong Daniel T. T.
Published: February 2019

Background

Routine use of pre‐participation electrocardiograms (ECGs) has been used by the Singapore Armed Forces, targeting early detection of significant cardiac diseases. We aim to describe the impact of demographic and anthropometric factors on ECG variables and establish a set of electrocardiographic reference ranges specific to a young male multiethnic Southeast Asian cohort.

Methods and results

Between November 1, 2009, and December 31, 2014, 144,346 young male conscripts underwent pre‐participation screening that included a 12‐lead ECG, demographic and anthropometric measurements. The Chinese population had the longest PR interval (146.7 ± 19.7 vs. 145.21 ± 19.2 in Malays vs. 141.2 ± 18.8 ms in Indians), QRS duration (94.5 ± 9.8 vs. 92.6 ± 9.7 in Malays vs. 92.5 ± 9.4 ms in Indians) and QTcB interval (408.3 ± 21.3 vs. 403.5 ± 21.6 in Malays vs. 401.2 ± 21.4 ms in Indians) (all p < 0.001). Body mass index (BMI) >25 kg/m2 and body fat >25% were independently associated with lower prevalence of increased QRS voltage on ECG. Systolic blood pressure of >140 mmHg or diastolic blood pressure of >90 mmHg independently increased the prevalence of increased QRS voltage on ECG.

Conclusions

Electrocardiographic parameters vary across different ethnicities and in comparison with international norms. In our population, diagnosis of increased QRS voltage by ECG is less prevalent with obesity and increased body fat. Further analysis of gold standard measurements for the diagnosis of LVH in our population is ongoing, to improve the accuracy of the ECG screening process.