bluuebunny/crossref_metadata_2025 huggingface dataset:
Within-Family Analysis of Interpregnancy Interval and Adverse Birth Outcomes [1G]
Authors: Class Quetzal A. , Oberg Anna S. , Sujan Ayesha C. , Almqvist Catarina , Larsson Henrik , D'Onofrio Brian
Published: April 2018

INTRODUCTION:

We examined the associations between interpregnancy interval, the duration from the preceding birth to the conception of the next-born index child, and adverse birth outcomes using designs that adjust for measured and unmeasured factors.

METHODS:

We used population-based Swedish registries to study a prospective cohort of children born 1973 to 2009 (n=1,418,820) to estimate the associations between interpregnancy interval and adverse birth outcomes. Analyses included cousin- and sibling-comparisons and postbirth intervals (i.e., the interval between second- and third-born offspring predicting second-born outcomes) to address unmeasured familial confounding.

RESULTS:

Traditional cohort-wide analyses showed higher odds of preterm birth (PTB) [adjusted odds ratio (aOR) 1.51, 99% CI 1.39-1.63] and low birth weight (LBW; aOR 1.25, 99% CI 1.13-1.39) after short interpregnancy interval (0 to 5 months) compared to offspring born after an interpregnancy interval of 18 to 23 months. Except for PTB (aOR 1.72, 99% CI 1.26-2.35), associations were attenuated in cousin- and sibling-comparisons. For interpregnancy intervals of 60 months or more, odds of PTB (aOR 1.51, 99% CI 1.43-1.60), LBW (aOR 1.61, 99% CI 1.50-1.73), and SGA (aOR 1.54, 99% CI=1.42-1.66) were higher when compared with the reference interval. Associations between long interpregnancy interval and adverse birth outcomes, however, remained through cousin- and sibling-comparisons. Postbirth interval analyses showed familial confounding is present for short interpregnancy intervals, but supported independent associations for long interpregnancy intervals.

CONCLUSION:

Familial confounding explains most of the association between short interpregnancy interval and adverse birth outcomes, while associations with long interpregnancy intervals were independent of measured and unmeasured factors.
Experiences of Transgender Men in Accessing Care in Gynecology Clinics [24G]
Authors: Frecker Helena , Scheim Ayden , Leonardi Mathew , Yudin Mark
Published: April 2018

INTRODUCTION:

Transgender, or “trans,” individuals face barriers to accessing medical care, however little is known regarding trans men’s experiences in accessing gynecologic care in particular. This study sought to determine if trans men in Ontario avoid presenting for gynecologic care and to gain understanding of their experiences in accessing this care.

METHODS:

Trans men ≥18 years old and living in Ontario were invited to participate in an online questionnaire. The study poster with questionnaire URL was distributed in both physical and online spaces frequented by the trans community.

RESULTS:

Of 89 respondents, 84/87 (97%) reported using a pronoun different from that associated with their birth-assigned gender, 71/87 (82%) reported current or past testosterone use, and 46/85 (54%) had undergone gender confirming surgery. 72/78 (92%) felt anxious about seeking gynecologic care and 43/79 (54%) had avoided attending gynecologic care settings because they were trans, citing the following reasons: encountering gendered forms (50%), sitting in a waiting room with cis women (54%), being misgendered (59%), having to educate providers (70%), and undergoing the gynecologic exam itself (86%). Many respondents found the gynecologic exam physically (60%) and emotionally (75%) distressing. Respondents endorsed options for an improved exam experience, including providers using gender non-specific language (85%), explaining each step before it occurs (55%), and having a support person present (47%).

CONCLUSION:

This study has highlighted areas for improvement in care provision that can be adopted by gynecologic care providers in order to make the experiences of trans men more inclusive, safe, and positive.
Antibiotic Prophylaxis in Surgical Sterilization: Following the Recommendations [29G]
Authors: Saunders Kelley T. , Slaughter Geoffrey T. , Mercer Laura , Gerkin Richard
Published: April 2018

INTRODUCTION:

Surgical site infections are the most common surgical complication. Antibiotic administration perioperatively has been shown to reduce associated morbidity, however, indiscriminate use has been associated with adverse outcomes. Selective antibiotic prophylaxis guidelines have been published by the American College of Obstetricians and Gynecologists (ACOG) for gynecologic procedures. Little is known regarding adherence to these recommendations. The primary objective was to determine adherence to ACOG recommendations for antibiotic prophylaxis in surgical sterilization. The secondary objective was to evaluate the patterns and predictors of appropriate antibiotic prophylaxis.

METHODS:

A retrospective chart review of preoperative antibiotics for laparoscopic and hysteroscopic sterilization procedures was performed at a single institution, Banner University Medical Center - Phoenix (BUMCP), from 01/01/2014 to 12/31/2014. Descriptive data were analyzed using chi-squared for categorical variables and Student t-test for continuous variables. P-values <.05 were considered significant.

RESULTS:

Of 165 women who met inclusion criteria, 50.9% received antibiotic prophylaxis outside of ACOG guidelines. Patient age, race and insurance status were not predictive of inappropriate prophylaxis. Women who underwent hysteroscopic sterilization were less likely to receive inappropriate prophylaxis compared to laparoscopic sterilization (18.6% vs 68.9%, P<.001). Antibiotic administration was less likely in cases assisted by lower-level residents compared to cases assisted by upper-level residents (46.4% vs 69.4%, P=.02). The number of years of attending experience was not predictive of adherence.

CONCLUSION:

There is widespread misuse of perioperative antibiotics for surgical sterilizations. Increased education and quality improvement is needed within BUMCP (our institution) to align practice patterns with evidence based recommendations.
Pregnant Women's Attitudes Toward Zika Virus Vaccine Study Participation [8J]
Authors: Goldfarb Ilona , Jaffe Elana , Lyerly Anne
Published: April 2018

INTRODUCTION:

Preventing Zika Virus (ZIKV) infection by vaccinating women may decrease risk of congenital Zika syndrome. Clinical trials are underway for inactivated, live attenuated, and DNA ZIKV vaccines. We sought to describe pregnant women’s attitudes toward participation in ZIKV vaccine research involving different vaccine platforms and to identify participation predictors and barriers.

METHODS:

Women attending prenatal care in June and July 2017 were offered enrollment in an anonymous survey which asked women their views about participating in hypothetical ZIKV vaccine research scenarios during pregnancy. Demographics and Zika exposure during pregnancy were obtained.

RESULTS:

Of 129 women, 70% expressed concern about ZIKV infection during pregnancy and 44% changed travel plans. Given the study scenarios, 68% stated they would consider an inactivated vaccine trial compared to 19% willing to participate in a live attenuated vaccine trial (p-value <0.0001). DNA vaccine trial acceptance was 51.6%. 57% of women believed the inactivated vaccine during pregnancy was safe for their baby compared to 26% for a live attenuated (p-value 0.012). Willing trial participants were most motivated by a desire to protect their babies from ZIKV, fewer were strongly motivated by a desire to contribute to science.

CONCLUSION:

Inclusion of pregnant women in ZIKV vaccine trials is imperative to ensure vaccines are safe, effective, and acceptable in pregnancy. A majority of women in our cohort would accept participation in inactivated and DNA vaccine trials during pregnancy while fewer would participate in a trial of a live attenuated vaccine. Understanding women’s motivations for trial participation is critical to vaccine trial design.
Report: Nursing Homes Are Overmedicating People with Dementia
Authors: Stockwell Serena
Published: April 2018

Laws against such ‘chemical restraints’ aren't being enforced.
NSAID Users Often Exceed Recommended Dose Limits
Authors: Mechcatie Elizabeth
Published: April 2018

Study reveals a poor understanding of label cautions and recommendations.
My People, 2014
Authors: Moore Amy Kenefick
Published: April 2018

A nurse with a gravely injured family member taps a hidden network of support.
Metabolism of the oocyte and the preimplantation embryo: implications for assisted reproduction
Authors: Scott Richard , Zhang Man , Seli Emre
Published: April 2018

Purpose of review

To discuss the common aspects of energy generation in the cell, substrate utilization by the oocyte and the preimplantation embryos, metabolic characteristics of the reproductive tract, and how metabolic characteristics of an embryo can be exploited to assess viability.

Recent findings

Utilization of pyruvate, lactate and glucose by the oocyte and the preimplantation embryo seems to be tightly controlled by the most essential molecular regulatory pathways.

Accumulating data on the metabolic needs of the preimplantation embryo and the substrate concentrations in the reproductive tract guide us in improving in-vitro culture conditions, and provide potential biomarkers of embryo viability.
Fertility, IVF and reproductive genetics
Authors: Varela Elisa , Sánchez-de-Puerta Irene , García-Velasco Juan A.
Published: April 2018

Purpose of review

Telomere attrition and dysfunction has become a well established pathway involved in organismal aging, not only because it imposes a limitation to cell division and therefore, tissue regeneration but also because telomere homeostasis influences other pathways involved in aging. However, the implication of telomere biology in ovarian aging and fertility is barely starting to be unveiled.

Recent findings

During the last years, mounting evidence in favor of the relationship between the accumulation of short telomeres and ovarian senescence has emerged. Telomere attrition and the loss of telomerase activity in ovarian cell types is a common characteristic of female infertility.

Recent findings regarding telomere attrition in the ovary open the possibility of both, finding new molecular biomarkers related to telomere homeostasis that make possible the early detection of ovarian dysfunction before the ovarian reserve has vanished, and the search of new therapies to preserve or set up ovarian cell types so that new and better quality oocytes can be generated in aged ovaries to improve IVF outcomes.
The case against endometrial ablation for treatment of heavy menstrual bleeding
Authors: Louie Michelle , Wright Kelly , Siedhoff Matthew T.
Published: April 2018

Purpose of review

Endometrial ablation is a common treatment for heavy menstrual bleeding, but serious limitations and long-term complications exist. Our purpose is to summarize the use of endometrial ablation devices, potential short-term and long-term complications, cost effectiveness, and quality of life in relation to alternative treatments.

Recent findings

There is insufficient evidence to strongly recommend one endometrial ablation device over another. Providers should consider and discuss with their patients, complications including risk of future pregnancy, endometrial cancer, and hysterectomy for continued bleeding or pain. Patient selection is key to reducing postablation pain and failure; patients with a history of tubal ligation and dysmenorrhea should consider alternative treatments. All patients should also be counseled that the levonorgestrel intrauterine device is a cost-effective alternative with higher quality of life and fewer complications. Hysterectomy is definitive treatment with higher quality of life and fewer complications.

Although endometrial ablation can offer adequate symptom control for patients who have failed medical therapy, desire uterine preservation, or who are high-risk surgical candidates, patients should be appropriately selected and counseled regarding the potential for treatment failure and long-term complications.
Frequency of Complications During Preparation of Corneal Lamellae Used in Posterior Lamellar Keratoplasty Using the Pneumodissection Technique (Big Bubble)
Authors: Studeny Pavel , Netukova Magdalena , Hlozanek Martin , Bednar Jan , Jirsova Katerina , Krizova Deli
Published: April 2018

Purpose:

To determine the frequency of formation of various types of bubbles and the potential impact of donor and lamella parameters on this frequency, and to identify possible risk factors of unsuccessful “big-bubble” creation in preparation of pre-Descemet endothelial keratoplasty and Descemet membrane endothelial keratoplasty with peripheral stromal support.

Methods:

Donor age and sex, death to preservation time (DPT), storage time, presence of corneal scars (mainly a condition after cataract surgery), and endothelial cell density of 256 donor corneas were assessed before Descemet membrane endothelial keratoplasty with peripheral stromal support or pre-Descemet endothelial keratoplasty lamella preparation using the big-bubble technique.

Results:

Mean donor age was 62.3 ± 8.5 years (28.3% women and 71.7% men). Mean endothelial cell density of the donor graft was 2866 ± 255 cells/mm2. Mean DPT was 10.12 ± 4.88 hours, and mean storage time of the transplant before surgery was 6.5 ± 4.8 days. Corneal scars were present in 17 donor grafts (6.6%) after cataract surgery. Eleven corneas were devalued because of Descemet membrane rupture during preparation (4.3%). In 182 corneas, standard bubble type I was created (71.7%); in 27 corneas, bubble type II was created; eventually, both types of bubbles formed simultaneously (10.5%); in 47 corneas, no bubble was created (18.4%).

Conclusions:

We identified higher endothelial cell density, shorter DPT, and the presence of corneal scars after cataract surgery as risk factors threatening successful bubble formation. The only risk factor for creating type II bubbles was higher donor age in our study.
Exploring Women’s Support Needs After Breast Reconstruction Surgery
Authors: Carr Tracey L. , Groot Gary , Cochran David , Vancoughnett Mikaela , Holtslander Lorraine
Published: April 2018

Background

The procedures for breast reconstruction (BR) after mastectomy frequently initiate a difficult recovery period. A better understanding of women’s support needs after surgery would improve patient care.

Objective

The aim of this study was to identify patients’ support needs after BR.

Methods

In a retrospective study design, 21 participants described their support experiences after BR, including their sources of support and the impact of support on their recovery in a semistructured interview. Transcriptions of the interviews were analyzed using thematic analysis.

Results

Four support needs were identified and were composed of elements of instrumental, emotional, and informational support. These needs were addressed to varying degrees by healthcare providers, family members, and other women who had BR experience.

Conclusion

Women’s experience of BR and their ability to cope are markedly better when their support needs are effectively addressed. Greater attention to their needs for support has the potential to improve patient care.

Implications for Practice

Nurses play a pivotal role in providing information to women who are recovering from BR. Improved access to communication channels between nurses and patients would likely improve patients’ support experiences. In addition, nurses can assess the women’s specific support needs and partner with families to help them understand how best to support women during recovery.
Efficacy of Reminiscence Therapy on Cognitive Functioning in Older Adults
Authors: Lin Li-Jung , Yen Hsin-Yen
Published: April 2018

Both life review programs and horticulture are beneficial for older adults' cognitive functioning. The purpose of this study was to examine the cognitive effects of reminiscence therapy. Participants older than 65 years in a day care center were recruited, and 14 of 24 participants were assigned to an experimental group. The intervention was based on Erickson's life stages and using plant lives as a metaphor for a human's life from birth to death. The intervention program was designed for 7 weeks of seven 1-hour sessions. The results demonstrated that the subscale scores of Orientation and Memory in the experimental group improved significantly. Total scores of the Loewenstein Occupational Therapy Cognitive Assessment were significantly improved in the experimental group following the intervention. Reminiscence therapy has cognitive benefits for older adults. The Horticultural Life Review Program is recommended for promoting older adults' psychological health.
Issues on Health Care for People With Parkinson's Disease in Korea
Authors: Lee JuHee , Yoo Yonju , Ahn Sangwoo , Choi MoonKi
Published: April 2018

It is important to fully appreciate perceptions of the physical, emotional, and social effects of Parkinson's disease (PD), which is progressive and complex. This is a qualitative study with focus group interviews to understand patients' challenges and needs relating to health care in PD. Thematic analyses were applied to analyze the qualitative data. There were 3 main themes, that is, “physical challenges,” “psychosocial response,” and “family relationships,” and 8 subthemes. These findings suggest that health care providers should be aware of specific patients' difficulties and needs to provide timely and appropriate interventions for people with PD.
Effect of Neuromuscular Electrical Stimulation on Labial and Lingual Weakness
Authors: Safi Mohammed F. , Wright-Harp Wilhelmina , Lucker Jay R. , Payne Joan C. , Harris Ovetta
Published: April 2018

Objective:

This study explored the effect of facial and submental neuromuscular electrical stimulation (NMES) in individuals with lingual, labial and buccal weakness.

Method:

An ABC/ACB design was used. Two male participants who acquired cerebrovascular accident (60 years) involved in this study. Both engaged in 2 treatment phases. One phase included performing an oral motor exercise program in conjunction with the NMES. Second phase included performing only oral motor exercise program.

Results:

Submental NMES did not have any effect on lingual strength. However, facial NMES had positive effect on labial strength in the 2 participants.
Analysis of 2 Operational Criteria Related to Muscle Loss in Elderly Brazilian Women
Authors: Lustosa Lygia Paccini , Batista Patrícia Parreira , Ribeiro-Samora Giane Amorim , Assis Marcella Guimarães , de Oliveira Ennes Thais , Scianni Aline Alvim
Published: April 2018

The aim of this study was to evaluate 2 operational criteria of the muscle loss adjusted to the body mass index in relation to the discriminative values for muscle mass corrected by height, in elderly Brazilian women. Muscle function (handgrip strength and gait speed) and body composition (dual-energy x-ray absorptiometry) were evaluated. A total of 112 elderly women (mean, 76.42 years; standard deviation, 6.53 years) participated of this study. The muscle loss index adjusted to the body mass was not capable of identifying elderly participants with muscle loss, as muscle mass corrected by height, with an area under the receiver operating characteristic curve of 0.52. There was no significance after the concordance analysis (κ= 0.03, P = .73). The handgrip strength was higher in the nonsarcopenic group when we used the muscle loss index adjusted to the body mass (P <.01). Other comparisons were not significant (P > .05). There was a significant difference in the proportions of sarcopenic patients between groups (P = .01).
Nutrition-Focused Physical Examination Practices of Registered Dietitian Nutritionists Who Have Completed an In-Person NFPE Course
Authors: Desjardins Susan , Brody Rebecca , Touger-Decker Riva
Published: April 2018

This study explored nutrition-focused physical examination (NFPE) practices of registered dietitian nutritionists (RDNs) who completed an in-person NFPE course. Relationships between NFPE conduct and professional characteristics of respondents were also investigated using a mixed-mode survey. Ninety-six respondents met the inclusion criteria. Examination of muscle, fat loss, hair/nails, weight, peripheral edema, skin, and height was the most frequently reported independent task. Time and workload were limitations to NFPE. Respondents with additional NFPE training conducted significantly more NFPE components independently (P = .002) than those without more training. Further research is needed with a larger sample of registered dietitian nutritionists who completed NFPE training.
Phase Angle Is Positively Associated With Handgrip Strength in Hospitalized Individuals
Authors: Reis Bianka C. A. , de Branco Flávia M. S. , Pessoa Debora F. , Barbosa Cinthia D. , dos Reis Aline S. , de Medeiros Luciana A. , de Oliveira Erick P.
Published: April 2018

The biological meaning of phase angle (PhA) is not well known, and one determinant of PhA might be muscle function. However, the research is still in its infancy. The aim of this study was to evaluate the association of PhA with handgrip strength (HGS) in hospitalized individuals. We conducted a cross-sectional study evaluating 139 patients older than 18 years who were admitted to a university hospital. Weight, height, circumferences, and skinfolds were measured. In addition, PhA was estimated by bioelectrical impedance and HGS was measured using a dynamometer. Individuals were classified for lower PhA (median values; <6.0° for women and <5.7° for men) and low HGS (<20 kg for women and <30 kg for men). We found that PhA was positively correlated with HGS (r = 0.54; P < .05), and after regression analysis, PhA was able to predict 29% of the variance in HGS. In addition, it was noted that individuals with lower PhA values presented with higher odds to have low HGS values (OR = 4.152; 95% CI, 1.854-9.295). Thus, PhA was positively associated with HGS, suggesting that PhA might be used as a predictor of muscle strength in hospitalized patients.
An examination of multivariable Mendelian randomization in the single sample and two-sample summary data settings
Authors: Sanderson Eleanor , Davey Smith George , Windmeijer Frank , Bowden Jack
Published: April 2018

Background

Mendelian Randomisation (MR) is a powerful tool in epidemiology which can be used to estimate the causal effect of an exposure on an outcome in the presence of unobserved confounding, by utilising genetic variants that are instrumental variables (IVs) for the exposure. This has been extended to Multivariable MR (MVMR) to estimate the effect of two or more exposures on an outcome.

Methods/Results

We use simulations and theory to clarify the interpretation of estimated effects in a MVMR analysis under a range of underlying scenarios, where a secondary exposure acts variously as a confounder, a mediator, a pleiotropic pathway and a collider. We then describe how instrument strength and validity can be assessed for an MVMR analysis in the single sample setting, and develop tests to assess these assumptions in the popular two-sample summary data setting. We illustrate our methods using data from UK biobank to estimate the effect of education and cognitive ability on body mass index.

Conclusion

MVMR analysis consistently estimates the effect of an exposure, or exposures, of interest and provides a powerful tool for determining causal effects in a wide range of scenarios with either individual or summary level data.
Assignment of the resting state of the secondary active transporter BetP by integrating spectroscopic measurements and molecular simulations
Authors: Leone Vanessa , Waclawska Izabela , Koshy Caroline , Kossman Katharina , Sharma Monika , Prisner Thomas F , Ziegler Christine , Endeward Burkhard , Forrest Lucy R
Published: April 2018

The glycine betaine symporter BetP regulates the osmotic stress response of Corynebacterium glutamicum, a soil bacterium used extensively in biotechnology. Although BetP is a homotrimer, biochemical studies have shown that each protomer is able to transport its substrate independently. Crystallographic structures of BetP have been determined in several conformations, seemingly capturing outward-open, inward-open and occluded states, both loaded with the substrate and in the apo form. However, it has been challenging to establish a correspondence between each of these structures and specific states in the mechanism of the transporter under more physiological conditions. To this end, we examined the dynamics of spin-labelled BetP using pulsed electron-electron double resonance (PELDOR) under different stimuli. We then carried out molecular simulations of structures of the BetP monomer to interpret the PELDOR data, using the enhanced-sampling methodology EBMetaD [Marinelli & Faraldo-Gomez, 2015, Biophys J 108(12):2779-2782], whereby the dynamics of the protein are minimally biased so as to reproduce the experimental data. Comparison of the magnitude of the biasing work required for different input structures permitted us to assign them to specific states of the transport cycle under each of the experimental conditions. In particular, this analysis showed that BetP adopts inward-facing conformations in the presence of excess sodium, and a mixture of states when betaine is added. These studies better delineate the major conformations adopted by BetP in its transport cycle, and therefore provide important insights into its mechanism. More broadly, we illustrate how integrative simulations can aid interpretation of ambiguous structural and spectroscopic data on membrane proteins.
Colistin resistance prevalence in Escherichia coli from domestic animals in intensive breeding farms of Jiangsu Province, China
Authors: Zhang X. , Zhang B. , Yu Z. , Guo Y. , Wang J. , Zhao P. , Liu J. , He K.
Published: April 2018

The global dissemination of colistin resistance has received a great deal of attention. Recently, the plasmid-mediated colistin resistance encoded by mcr-1 and mcr-2 genes in Escherichia coli (E.coli) strains from animals, food, and patients in China have been reported continuously. To make clear the colisin resistance and mcr gene spread in domestic animals in Jiangsu Province, we collected fecael swabs from pigs, chicken and cattle at different age distributed in intensive feeding farms. The selected chromogenic agar and mcr-PCR were used to screen the colisin resistance and mcr gene carriage. Colistin resistant E.coli colonies were identified from 54.25 % (440/811) pig faecal swabs, from 35.96 % (443/1232) chicken faecal swabs, and 26.92 % (42/156) from cattle faecal swabs. Of all the colisin resistant E.coli colonies, the positive amplifications of mcr-1 were significantly higher than mcr-2. The mcr-1 prevalence was 68.86 % (303/440) in pigs, 87.58 % (388/443) in chicken, and 71.43 % (30/42), compared with 46.82 % (206/440) in pigs, 14.90 % (66/443) in chicken, and 19.05 % (8/42) in cattle of prevalence of mcr-2. Co-occurrence of mcr-1 and mcr-2 was identified in 20 % (88/440) in pigs, 7.22 % (32/443) in chickens, and in 9.52 % (4/42) cattle. These data indicate that mcr was the most important colistin resistance mechanism. Interventions and alternative options are necessary to minimise further dissemination of mcr between food-producing animals and human.

IMPORTANCE

Colistin is recognized one of the last defence lines for the treatment of highly resistant bacteria, but the emergence of resistance that conferred by a transferable plasmid-mediated mcr genes to this vital antibiotic is extremely disturbing. Here, we used E. coli as an index to monitor drug resistance in domestic animals (pigs, chicken and cattle). It was found that the colistin resistance widely occurred at all ages of domestic animals and the mcr-dependent mechanism dominated in E.coli. We also found that the elder and adult animals were a reservoir of resistant strains, suggesting a potential food safety issue and greater public health problems.
From Synchrony to Asynchrony: Cerebellar-Basal Ganglia Functional Circuits in Young and Older Adults
Authors: Hausman Hanna K. , Jackson T. Bryan , Goen James R.M. , Bernard Jessica A.
Published: April 2018

Resting state functional magnetic resonance imaging (rs-fMRI) has indicated disruptions in functional connectivity in older (OA) relative to young adults (YA). While age differences in cortical networks are well studied, differences in subcortical networks are poorly understood. Both the cerebellum and the basal ganglia are of particular interest given their role in cognitive and motor functions, and work in non-human primates has demonstrated direct reciprocal connections between these regions. Here, our goal was twofold. First, we were interested in delineating connectivity patterns between distinct regions of the cerebellum and basal ganglia, known to have topologically distinct connectivity patterns with cortex. Our second goal was to quantify age-differences in these cerebellar-striatal circuits. We performed a targeted rs-fMRI analysis of the cerebellum and basal ganglia in 33 YA and 31 OA individuals. In the YA, we found significant connectivity both within and between the cerebellum and basal ganglia, in patterns supporting semi-discrete circuits that may differentially subserve motor and cognitive performance. We found a shift in connectivity, from one of synchrony in YA, to asynchrony in OA, resulting in substantial age differences. Connectivity was also associated with behavior. These findings significantly advance our understanding of cerebellar-basal ganglia interactions in the human brain.
A conservation assessment of the freshwater gastropods of South Dakota based on historical records and recent observations
Authors: Stephen Bruce J.
Published: April 2018

In South Dakota, like most U.S. states, up-to-date knowledge of the distribution of freshwater gastropod species is lacking and historical data suffers from a host of synonyms. I consulted literature records and online museum databases to compile a list of freshwater gastropods historically recorded for South Dakota. I used systematic studies and regional records to evaluate each historically-listed species reducing 54 nominal species to 25 expected to inhabit South Dakota. This, along with recent survey data from across the state, enable a benchmark conservation status to be established for the freshwater gastropods of South Dakota. My preliminary conservation evaluation indicatesPlanorbula armigerais critically imperiled (S1), while three species;Ferrissia rivularis, Campeloma decisum, andAmnicola limosusare imperiled (S2). The status of historical species not observed recently, and suspected inhabitants known from adjacent states are discussed.
A rapid and robust method for single cell chromatin accessibility profiling
Authors: Chen Xi , Miragaia Ricardo J , Natarajan Kedar Nath , Teichmann Sarah A
Published: April 2018

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is widely used to identify regulatory regions throughout the genome. However, very few studies have been performed at the single cell level (scATAC-seq) due to technical challenges. Here we developed a simple and robust plate-based scATAC-seq method, combining upfront bulk Tn5 tagging with single-nuclei sorting. We demonstrated that our method worked robustly across various systems, including fresh and cryopreserved cells from primary tissues. By profiling over 3,000 splenocytes, we identify distinct immune cell types and reveal cell type-specific regulatory regions and related transcription factors.
Laboratory evolution from social to solitary behavior in the N2 reference strain is unnecessary for its fitness advantages
Authors: Zhao Yuehui , Long Lijiang , Xu Wen , Campbell Richard F. , Large Edward L. , Greene Joshua S. , McGrath Patrick T.
Published: April 2018

The standard reference Caenorhabditis elegans strain, N2, has evolved marked behavioral changes since its isolation from the wild 67 years ago. Laboratory-derived variation in two genes, npr-1 and glb-5, suppress aerotaxis behaviors on food, resulting in N2 animals evolving from social to solitary feeding strategies. We show here that the derived alleles of npr-1 and glb-5 can confer large fitness advantages in standard laboratory conditions, suggesting that the changes in feeding strategies were beneficial to the N2 strain. However, by using environmental manipulations that suppress social behaviors, we showed the fitness advantages of the derived alleles remained unchanged, suggesting selection on these alleles acted through biological traits unrelated to solitary behavior. Transcriptomics analysis, developmental timing assays, and feeding assays showed that N2 animals mature faster, produce more sperm, and eat more food than a strain containing ancestral alleles of these genes (CX12311) regardless of the behavioral strategies. The O2-sensing neurons URX, AQR, and PQR and the pheromone biosynthesis and lipid regulating enzyme encoded by daf-22 are necessary for the full fitness advantages. We suggest that changes to social/solitary behavior in N2 were a pleiotropic consequence of npr-1 and glb-5’s ability to modify integrated O2 and pheromone neural circuits that regulate feeding rate and reproductive development. Together, our results demonstrate how laboratory evolution can lead to profound changes in a strain used as a model by for understanding a variety of fundamental biological processes.
Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing
Authors: O'Flaherty Brigid M. , Li Yan , Tao Ying , Paden Clinton R. , Queen Krista , Zhang Jing , Dinwiddie Darrell L. , Gross Stephen M. , Schroth Gary P. , Tong Suxiang
Published: April 2018

Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the genomes, allowing for identification of known viruses and full genome sequencing, while the second set targets regions conserved among viral families or genera, providing the ability to detect both known and potentially novel members of those virus groups. Efficiency of enrichment was assessed by NGS testing reference virus and clinical samples with known infection. We show significant improvement in viral identification using enriched NGS compared to unenriched NGS. Without enrichment, we observed an average of 0.3% targeted viral reads per sample. However, after enrichment, 50%–99% of the reads per sample were the targeted viral reads for both the reference isolates and clinical specimens using both probe sets. Importantly, dramatic improvements on genome coverage were also observed following virus-specific probe enrichment. The methods described here provide improved sensitivity for virus identification by NGS, allowing for a more comprehensive analysis of disease etiology.
Correct interpretation of diffraction properties of quartz crystals for X-ray optics applications. Corrigendum
Authors: Huang Xian-Rong , Gog Thomas , Kim Jungho , Kasman Elina , Said Ayman H. , Casa Diego M. , Wieczorek Michael , Hönnicke Marcelo G. , Assoufid Lahsen
Published: April 2018

Errors about left-handed (laevorotatory) quartz and right-handed (dextrorotatory) quartz in the paper by Huang, Gog, Kim, Kasman, Said, Casa, Wieczorek, Hönnicke & Assoufid [J. Appl. Cryst. (2016), 51, 140–147] are corrected.
Towards generalized data reduction on a chopper-based time-of-flight neutron reflectometer
Authors: Gutfreund Philipp , Saerbeck Thomas , Gonzalez Miguel A. , Pellegrini Eric , Laver Mark , Dewhurst Charles , Cubitt Robert
Published: April 2018

The calculation of neutron reflectivity from raw time-of-flight data including instrumental corrections and an improved resolution calculation is presented. The theoretical calculations are compared with experimental data measured on the vertical sample plane reflectometer D17 and the horizontal sample plane reflectometer FIGARO at the Institut Laue–Langevin (ILL), Grenoble, France. This article comprises the mathematical body of the time-of-flight reflectivity data-reduction software COSMOS which is used on D17 and FIGARO.
Quanty4RIXS: a program for crystal field multiplet calculations of RIXS and RIXS–MCD spectra usingQuanty
Authors: Zimmermann Patric , Green Robert J. , Haverkort Maurits W. , de Groot Frank M. F.
Published: April 2018

Some initial instructions for theQuanty4RIXSprogram written in MATLAB®are provided. The program assists in the calculation of 1s 2p RIXS and 1s 2p RIXS–MCD spectra usingQuanty. Furthermore, 1s XAS and 2p 3d RIXS calculations in different symmetries can also be performed. It includes the Hartree–Fock values for the Slater integrals and spin–orbit interactions for several 3dtransition metal ions that are required to create the .lua scripts containing all necessary parameters and quantum mechanical definitions for the calculations. The program can be used free of charge and is designed to allow for further adjustments of the scripts.
From urban exploration to ruin tourism: a geographical analysis of contemporary ruins as new frontiers for urban tourism
Authors: Le Gallou Aude
Published: April 2018

Purpose

Despite the increasing academic interest for urban ruins and evolutions of urban tourism, research on ruin tourism as an emergent form of urban tourism practice is still lacking. Drawing on existing works on urban exploration, the purpose of this paper is to provide a first geographical insight into ruin tourism and its spatial implications in terms of imaginaries, practices and regulation of urban space.

Design/methodology/approach

Drawing on an urban and cultural geography approach, the research is based on a mix of empirical methodologies. Participant observation of organized ruin tours as well as formal and informal interviews with participants, organizers, institutional actors and inhabitants have been conducted during fieldwork completed in Berlin and Detroit. This paper also draws on the analysis of additional data provided by online material, especially official websites of tour organizers, forum threads and comments posted on different websites.

Findings

The research shows that ruin tourism can be analyzed as a new practice of urban tourism based on the reappropriation and commodification of alternative practices developing in marginalized urban areas. The paper provides evidence of ruin tourism’s contribution to the normalization of urban space through tourism conquest of new urban territories. It also shows that the practice fosters contested material and symbolic appropriations of place.

Originality/value

This paper contributes to current research on alternative tourism practices in marginalized urban areas as well as on tourist appropriation of liminal spaces. It provides a first analysis of ruin tourism and underscores its potential as a geographical object for the investigation of a wide range of urban issues.
Global supply chain network design problem with rules of origin and limited import quotas
Authors: Cheng Xinxuan , Yang Guoqing , Fan Longfei
Published: April 2018

Purpose

This paper aims to develop an uncertain global supply chain network design (GSCND) model with rules of origin (RoOs) and limited import quotas, and to discuss the international factors’ effects on location decisions.

Design/methodology/approach

The authors establish an uncertain GSCND model with the international factors. The transportation costs and customers’ demands are characterized as random variables. To deal with the risk of uncertainty, the authors introduce the customers’ demand service level. A sample approximation approach (SAA) is used to deal with the service level constraint and turn the proposed model into a mixed integer programming. On the basis of the properties of the proposed model, a hybrid memetic algorithm (MA) is designed to solve it.

Findings

The authors find that the proposed MA is efficient to the real supply chain network design problem. Besides, the RoOs and limited import quotas can affect the optimal choices of plant and distribution center locations.

Originality/value

The authors propose an uncertain GSCND model with RoOs and limited import quotas. An MA with SAA is designed to solve the proposed model. The authors apply the proposed model into a real global supply chain of an apparel corporation in East Asia, and give some managerial insights.
Mining reference chat transcripts to analyze noise complaints
Authors: Vance Jason M.
Published: April 2018

Purpose

This case study provides a new methodology for examining patron-initiated noise complaints in academic libraries by mining virtual reference chat transcript logs. The purpose of this study is to illustrate how noise complaints can be identified, analyzed and mapped to create a visual representation of the library’s soundscape.

Design/methodology/approach

This study reviewed 4,494 reference chat logs taken over four semesters at a large public university between August 2015 and May 2017. From these transcripts, the author identified 330 unique noise complaints and analyzed them by content, time of day, day of week, week of semester and floor of library. Complaints were also plotted on a library map to determine noise complaint hot spots.

Findings

Analysis of the noise complaints showed that 82 per cent of the reported incidents originated in designated quiet study zones and 55 per cent of the complaints occurred in the evenings when the library was more lightly staffed. Mapping the noise complaints revealed that most infractions were reported in areas where public computing areas and group study rooms were situated directly adjacent to designated quiet study areas.

Originality/value

Although there are numerous studies on noise in libraries and many published analyses of reference chat transcripts, this paper is the first to analyze chat transcripts for the purpose of studying noise complaints in the library. This paper is an expansion of a preliminary study presented at the 2016 Library Assessment Conference in Arlington, VA.
Generosity, fairness, trust and time: the performance of therapeutic community residents in economics experiments
Authors: Gampa Anup , Linley Jessica V. , Roe Brian , Warren Keith L.
Published: April 2018

Purpose

Therapeutic communities (TCs) assume that residents are capable of working together to overcome substance abuse and criminal behavior. Economic games allow us to study the potential of cooperative behavior in TC residents. The paper aims to discuss this issue.

Design/methodology/approach

The authors analyze results from a sample of 85 corrections-based TC residents and a comparison group of 45 individuals drawn from the general population who participated in five well-known economic experiments – the dictator game, the ultimatum game, the trust game, risk attitude elicitation and time preference elicitation.

Findings

TC residents keep less money in the dictator game and return more in the trust game, and prefer short-term rewards in the time preference elicitation. In the ultimatum game, nearly half of all residents refuse offers that are either too low or too high.

Research limitations/implications

While the study involves a sample from one TC and a comparison group, the results suggest that residents are at least comparable to the general public in generosity and appear willing on average to repay trust. A substantial minority may have difficulty accepting help.

Practical implications

Rapid peer feedback is of value. Residents will be willing to offer help to peers. The TC environment may explain residents’ tendency to return money in the trust game. Residents who refuse to accept offers that are either too low or too high in the ultimatum game may also have difficulty in accepting help from peers.

Social implications

Economic games may help to clarify guidelines for TC clinical practice.

Originality/value

This is the first use of economic games with TC residents.
Training for democratic therapeutic community practitioners, and workers in therapeutic and enabling environments
Authors: Pearce Steve , Dale Oliver
Published: April 2018

Purpose

Training in therapeutic community and related approaches has not been widely available, and there is debate about the form this should take. This has had a negative impact on the field. The paper aims to discuss this issue.

Design/methodology/approach

The authors consider the history of training in democratic therapeutic community methods in the UK in particular, and trace some of the reasons for its lack of development.

Findings

With the expansion of TC methodology into new areas, such as therapeutic and enabling environments, the ability to provide training in DTC approaches and techniques is increasingly important. The developing evidence base, and the increasing detail in which the method has been described, make dedicated TC training increasingly important.

Originality/value

Training in therapeutic community methods, and enabling and therapeutic environment approaches, provides a grounding in technique and theory that would otherwise be impossible to acquire for most workers, and can lead to a general increase in the level of competence and confidence in the way these environments operate.
The application of microorganisms of phosphate providers and organic matters to improve the growth of Arabica coffee seedlings at Andisol in Bener Meriah Regency
Authors: Hifnalisa  , Sahar Asmarlaili , Sabrina T. , Nisa T. Chairun
Published: April 2018

Purpose

The purpose of this paper is to examine the effect of the application of microorganisms of phosphate providers and organic matters for the growth of Arabica coffee seedlings in Bener Meriah Regency.

Design/methodology/approach

The experiments were performed inside the screen house using a random design of factorial group with six repetitions. The experimental treatments consisted of two factors. Factor I is the application of microorganisms of phosphate providers. Factor II is the application of organic matters (T. diversifoliaand the coffee bean skins). The parameters observed were as follows: enhancement of plant height was observed every 30 days for 270 days, and a number of primary branch and dry weight of roots were observed 270 days after planting (DAP). The data obtained were analyzed by analyzing the variance at 5 per cent level; if the treatment had an effect, then the treatment was continued to Duncan’s multiple range test at 5 per cent.

Findings

The application of microorganisms of phosphate provider increases the height improvement, the number of primary branches and the dry weight of roots of Arabica coffee seedlings. The application ofListeriasp. microorganisms of phosphate provider gives the highest yield on the height increase, the number of primary branches and the dry weight of roots of Arabica coffee seedlings. The application of organic matters of coffee beans skin gives higher yield thanTithonia diversifoliain height and dry weight of roots of Arabica coffee seedlings. The interaction between the application of microorganisms of phosphate provider and organic matters increases the dry weight of roots of Arabica coffee seedlings. The interaction ofListeriasp.-skin of coffee beans gives the highest yield on dry weight of roots of Arabica coffee seedlings.

Originality/value

Several other studies have demonstrated that the application of microorganisms of phosphate providers using phosphate solubilizing bacteria (Fitriatin et al., 2014; Sembiring et al., 2017) and mycorrhizal use (Hart and Trevors, 2005; Rouphael et al., 2015) increased the growth and yield plant. No previous study comprehensively studied the application of microorganisms of phosphate providers and organic matters to improve the growth of Arabica coffee seedlings in Andisol in Bener Meriah Regency.