bluuebunny/crossref_metadata_2025 huggingface dataset:
Gender Development in Children with Gay, Lesbian, and Heterosexual Parents: Associations with Family Type and Child Gender
Authors: Carone Nicola , Lingiardi Vittorio , Tanzilli Annalisa , Bos Henny M. W. , Baiocco Roberto
Published: September 2019

Objective:

To examine whether the gender development of 120 Italian children (40 born to gay fathers [GFs] through surrogacy, 40 born to lesbian mothers [LMs] through sperm donation, and 40 born to heterosexual parents [HPs] through sexual intercourse) aged 3 to 9 years differed as a function of family type and/or child gender.

Methods:

Children took part in observed free-play sessions while primary caregivers and nonparent caregivers were administered standardized interviews. Hierarchical linear modeling, analysis of covariance, simple effects analysis, and bootstrapping were conducted.

Results:

Boys and girls of GFs and HPs were reported to show less gender flexibility in their activities and characteristics than boys and girls of LMs. They also received higher scores of gender conforming dress-up play and spent more time playing with gender-conforming toys. In all family types, boys and girls were reported to show low levels of gender-nonconforming dress-up play and observed to spend less time playing with gender-nonconforming toys. Overall, comparisons within genders indicated that boys and girls of GFs and HPs were considered more masculine and feminine, respectively, in their behavior and play, relative to boys and girls in LM families. Age was not a significant covariate in any analysis.

Conclusion:

Our findings do not support the idea that children of gay or lesbian parents show greater gender nonconformity relative to children of HPs. The findings are informative to those concerned with the effects of the absence of a male or female live-in parent on child gender development.
Treatment Outcomes Following Resident Performed Nonvalved (Baerveldt 350) Glaucoma Drainage Device Implantation
Authors: Rothman Adam L. , Rosdahl Jullia A. , Hunter Thomas G. , Challa Pratap , Muir Kelly W.
Published: September 2019

Precis:

When compared with outcomes by glaucoma specialists in several prospective studies, residents at the Durham Veterans Affairs Medical Center achieved comparable reductions in intraocular pressure (IOP) and failure rates during the year following Baerveldt drainage device implantation.

Purpose:

To review the outcomes of resident performed Baerveldt implantation through 1 year of postoperative management in a resident-run clinic.

Materials and Methods:

The medical records of all veterans at the Durham Veterans Affairs Medical Center were searched to identify those with Baerveldt implantation by resident physicians from July 1, 2007 to June 30, 2017. Exclusion criteria include previous glaucoma tube or concurrent surgical intervention, including cataract extraction. All postoperative visits were reviewed and clinical data were collected. Failure was defined as 2 consecutive visits, starting at postoperative month (POM) 3, with IOP ≤5 mm Hg, or with IOP >21 mm Hg or <20% IOP reduction from baseline, reoperation for glaucoma, or loss of light perception.

Results:

A total of 48 eyes were included with mean (SD) IOP and number of medications: baseline, 23.1 (6.7) mm Hg on 3.7 (1.0) medications; postoperative day 1, 20.5 (11.7) mm Hg on no medications; postoperative week 1, 14.3 (6.9) mm Hg and 1.9 (1.7) medications; POM1, 16.7 (6.4) mm Hg and 2.2 (1.5) medications; POM3, 15.1 (5.2) mm Hg and 2.1 (1.6) medications; POM6 12.8 (4.9) mm Hg and 2.8 (1.3) medications; POM12, 13.0 (4.0) mm Hg and 2.8 (1.4) medications. IOP decreased at all time intervals (P<0.01) but postoperative day 1 (P=0.15) while medication burden was reduced at every visit (P<0.01). Through 12 months, 8 patients (17%) failed with a time to failure of 9.2 (0.3) months. No patients underwent additional glaucoma surgical interventions or lost light perception.

Conclusions:

Residents can safely and efficaciously perform Baerveldt implantation, providing reassurance regarding the autonomy afforded residents in the operating room and clinic.
Anterior Segment Optical Coherence Tomography: Is There a Clinical Role in the Management of Primary Angle Closure Disease?
Authors: Nongpiur Monisha E. , Tun Tin A. , Aung Tin
Published: September 2019

Primary angle closure disease (PACD) covers a spectrum that includes primary angle closure suspect, primary angle closure, primary angle closure glaucoma, and acute primary angle closure. Accumulating evidence suggests that the pathogenesis of PACD is complex, with multiple contributory factors including variations in the anatomic or biometric characteristics of the angle segment structures. Advances in anterior segment optical coherence tomography technology have further enhanced our understanding of the risk factors and mechanisms involved in the disease process. This review discusses the potential clinical role of the anterior segment optical coherence tomography in the diagnosis, mechanistic evaluation, and as a predictor for future clinical outcomes of patients with PACD.
A Quality Improvement Project to Increase Mother’s Milk Use in an Inner-City NICU
Authors: Kalluri Nikita S. , Burnham Laura A. , Lopera Adriana M. , Stickney Donna M. , Combs Ginny L. , Levesque Bernadette M. , Philipp Barbara L. , Parker Margaret G.
Published: September 2019

Introduction:

Mother’s milk is recommended for preterm infants due to numerous health benefits. At our inner-city hospital, >80% of mothers of infants younger than 34 weeks’ gestation initiated milk production, but fewer continued until discharge. Among infants younger than 34 weeks’ gestation, we aimed to (1) increase any mother’s milk use in the 24 hours before discharge/transfer to >75%; (2) increase exclusive mother’s milk use in the 24 hours before discharge/transfer to >50%; and (3) reduce racial/ethnic disparities in mother’s milk use.

Methods:

We conducted a quality improvement project from January 2015 to December 2017 focused on prenatal education, first milk expression ≤6 hours after birth, and skin-to-skin care in the first month. We tracked process measures and main outcomes with run and control charts among 202 infants younger than 34 weeks’ gestation eligible to receive mother’s milk born at our hospital; We tracked results according to maternal race/ethnicity subgroups.

Results:

Forty-seven percent of mothers were non-Hispanic black, 28% were Hispanic, and 13% were non-Hispanic white. We improved the rate of first milk expression ≤6 hours after birth and skin-to-skin care in the first month but did not improve rates of any/exclusive mother’s milk use at discharge/transfer. Eight-five percent of infants had mothers that initiated milk production, but only 55% received any mother’s milk at discharge/transfer.

Conclusions:

Our single-center quality improvement effort focused on infants younger than 34 weeks’ gestation whose mothers were predominately Hispanic and non-Hispanic blacks. We successfully increased first milk expression ≤6 hours after birth and skin-to-skin care but did not increase mother’s milk use at discharge/transfer.
Certified Basic Life Support Instructors Identify Improper Cardiopulmonary Resuscitation Skills Poorly
Authors: Hansen Camilla , Bang Camilla , Stærk Mathilde , Krogh Kristian , Løfgren Bo
Published: September 2019

Introduction

During basic life support (BLS) training, instructors assess learners' cardiopulmonary resuscitation (CPR) skills and correct errors to ensure high-quality performance. This study aimed to investigate certified BLS instructors' assessments of CPR skills.

Methods

Data were collected at BLS courses for medical students at Aarhus University, Aarhus, Denmark. Two certified BLS instructors evaluated each learner with a cardiac arrest test scenario, where learners demonstrated CPR on a resuscitation manikin for 3.5 minutes. Instructors' assessments were compared with manikin data as reference for correct performance. The first 3 CPR cycles were analyzed. Correct chest compressions were defined as 2 or more of 3 CPR cycles with 30 ± 2 chest compressions, 50 to 60 mm depth, and 100 to 120 min−1 rate. Correct rescue breaths were defined as 50% or more efficient breaths with visible, but not excessive manikin chest inflation (for instructors) or 500 to 600mL air (manikin data).

Results

Overall, 90 CPR assessments were performed by 16 instructor pairs. Instructors passed 81 (90%) learners, whereas manikin pass rate was 2%. Instructors identified correct chest compressions with a sensitivity of 0.96 [95% confidence interval (CI) = 0.79–1) and a specificity of 0.05 (95% CI = 0.01–0.14), as well as correct rescue breaths with a sensitivity of 1 (95% CI = 0.40–1) and a specificity of 0.07 (95% CI = 0.03–0.15). Instructors mistakenly failed 1 learner with adequate chest compression depth, while passing 53 (59%) learners with improper depth. Moreover, 80 (89%) improper rescue breath performances were not identified.

Conclusions

Certified BLS instructors assess CPR skills poorly. Particularly, improper chest compression depth and rescue breaths are not identified.
In vitro model for resistance in oncogene-dependent tumors at the limit of radiological detectability
Authors: Müller Nina , Brägelmann Johannes , Lorenz Carina , Michel Ulrich P. , Plenker Dennis , Ortiz-Cuaran Sandra , Weiss Jonathan , Büttner Reinhard , Peifer Martin , Thomas Roman K. , Sos Martin L. , Berg Johannes
Published: September 2019

In solid tumors, the response to targeted therapy is typically short-lived, as therapy-resistant mutants can quickly expand during therapy. Here we analyze the spectrum of such resistance mutations coexisting in a large population of cancer cells. We use an iterative scheme of artificial evolution to amplify and isolate different resistance mechanisms. As a proof of concept, we apply our scheme to PC-9 cells, a human non-small cell lung cancer cell line with an activating EGFR mutation. The mechanisms we find comprise the well-known gatekeeper-mutation T790M in EGFR, a mutation in NRAS, the amplification of MET-ligandHGF, as well as induction of AKT-mTOR signaling. In this model, a combination of four drugs targeting these mechanisms prevents not only the expansion of resistant cells, but also inhibits the growth of drug-tolerant cells, which can otherwise act as a reservoir for further resistance mutations. These data suggest that a finite number of drugs specifically acting on individual resistant clones may be able to control resistance in oncogenically driven lung cancer.
Species and sex divergence in vocalizations between hybridizing role-reversed shorebirds, Northern Jacana(Jacana spinosa)and Wattled Jacana(Jacana jacana)
Authors: Buck Evan J. , Brown Toni , Zwicky Gina , Derryberry Elizabeth P. , Lipshutz Sara E.
Published: September 2019

Species-specific vocalizations can act as a reproductive isolating mechanism between closely related populations. We analyzed vocal divergence between two hybridizing species of sex-role reversed polyandrous shorebirds, the Northern Jacana (Jacana spinosa) and Wattled Jacana (Jacana jacana). We found thatJ. spinosacalls have higher peak frequency and fundamental frequency thanJ. jacanacalls. We also compared calls between males and females, as both jacana species are sex-role reversed and females compete for male mates. Males produce calls with a higher peak frequency, exhibit shorter note lengths and emit a greater number of notes within a calling bout than females, which could relate to mate attraction. These results suggest that vocal divergence could act as a behavioral barrier to limit hybridization between the species and vocalizations may function differently between male and female jacanas.
GISA: Using Gauss Integrals to identify rare conformations in protein structures
Authors: Grønbæk Christian , Hamelryck Thomas , Røgen Peter
Published: September 2019

The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations.

We here propose a general method which transforms a structure into a “fingerprint of topological-geometric values” consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is therefore not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general. To achieve this our new algorithm, GISA, as a key novelty produces the descriptors, so called Gauss integrals, not only for the full chains of a protein but for all its sub-chains, thereby allowing fingerprinting on any scale from local to global. The Gauss integrals are known to be effective descriptors of global protein folds.

Applying GISA to a set of about 8000 high resolution structures (top8000), we first show how it enables swift identification of predefined geometries such as pokes and links. We then apply GISA with no restrictions on geometry, to show how it allows identifying rare conformations by finding rare invariant values only. In this unrestricted search, pokes and links are still found, but also knotted conformations, as well as more highly entangled configurations not previously described. Thus, applying the basic scan method in GISA’s tool-box to the top8000 set, 10 known cases of knots are ranked as the top positive Gauss number cases, while placing at the top of the negative Gauss numbers 14 cases in cis-trans isomerases sharing a spatial motif of little secondary structure content, which possibly has gone unnoticed.

Potential applications of the GISA tools include finding errors in protein models and identifying unusual conformations that might be important for protein folding and function. By its broad potential, we believe that GISA will be of general benefit to the structural bioinformatics community.

GISA is coded in C and comes as a command line tool. Source and compiled code for GISA plus read-me and examples are publicly available at GitHub (https://github.com).
High-throughput fluorescence-based screen identifies the neuronal microRNA miR-124 as a positive regulator of alphavirus infection
Authors: López Paula , Girardi Erika , Mounce Bryan C. , Weiss Amélie , Chane-Woon-Ming Béatrice , Messmer Mélanie , Kaukinen Pasi , Kopp Arnaud , Bortolamiol-Becet Diane , Fendri Ali , Vignuzzi Marco , Brino Laurent , Pfeffer Sébastien
Published: September 2019

Micro (mi)RNAs are small regulatory RNAs, which act as guide for the RISC complex to modulate the expression of target genes. In addition to their role in maintaining essential physiological functions in the cell, miRNAs can also regulate viral infections. They can do so directly by targeting RNAs of viral origin or indirectly by targeting RNAs from the host and this can result in a positive or negative outcome for the virus. Here, we performed a miRNA genome-wide screen in order to identify cellular miRNAs involved in the regulation of arbovirus infection in human cells. We identified sixteen miRNAs showing a positive effect on the virus, among which a number of neuron-specific ones such as miR-124. We confirmed that overexpression of miR-124 increases Sindbis virus (SINV) viral production and that this effect is mediated by its seed sequence. We further demonstrated that the SINV genome possesses a binding site for miR-124-3p. Both inhibition of miR-124-3p or silent mutations to disrupt this binding site in the viral RNA abolished the positive regulation. We also proved that miR-124 inhibition reduces SINV infection in human differentiated neuronal cells. Finally, we showed that the proviral effect of miR-124 is conserved for other medically relevant alphaviruses. Indeed, inhibition of miR-124 expression reduces chikungunya virus (CHIKV) viral production in human cells. Altogether, our work expands the panel of positive regulation of the viral cycle by direct binding of host miRNAs to the viral RNA and provides new insights into the role of cellular miRNAs as regulators of alphavirus infection.

SIGNIFICANCE STATEMENT

Arthropod-borne (arbo) viruses are part of a class of pathogens that are transmitted to their final hosts by insects. Because of climate change, the habitat of some of these insects, such as mosquitoes, is shifting, thereby facilitating the emergence of viral epidemics. Among the pathologies associated with arboviruses infection, neurological diseases like meningitis or encephalitis represent a significant health burden. Using a genome-wide miRNA screen, we identified the neuronal miR-124 as a positive regulator of the Sindbis and chikungunya alphaviruses. We also showed that this effect was in part direct, thereby opening novel avenues to treat alphaviruses infection.
Positive and negative intra-molecular modulation in a dual-cassette RNA helicase
Authors: Vester Karen , Santos Karine F. , Kuropka Benno , Weise Christoph , Wahl Markus C.
Published: September 2019

RNA helicase Brr2 is required for the activation of the spliceosome prior to the first catalytic step of splicing. Brr2 represents a distinct subgroup of Ski2-like nucleic acid helicases whose members comprise tandem helicase cassettes. Only the N-terminal cassette of Brr2 is an active ATPase and can unwind substrate RNAs. The C-terminal cassette represents a pseudo-enzyme that can stimulate RNA-related activities of the N-terminal cassette. However, the molecular mechanisms, by which the C-terminal cassette modulates the activities of the N-terminal unit remain elusive. Here, we show that N- and C-terminal cassettes adopt vastly different relative orientations in a crystal structure of Brr2 in complex with an activating domain of the spliceosomal Prp8 protein as compared to the crystal structure of isolated Brr2. Likewise, the cassettes occupy different relative positions and engage in different inter-cassette contacts during different stages of splicing. Engineered disulfide bridges that lock the cassettes in two different relative orientations have opposite effects on RNA-related activities of the N-terminal cassette compared to the unrestrained protein. Moreover, different relative positioning of the cassettes strongly influences ATP hydrolysis by the N-terminal cassette. Our results demonstrate that the inactive C-terminal cassette of Brr2 can exert both positive and negative influence on the active N-terminal helicase unit from a distance.
Comparative genomics unravels mechanisms of genetic adaptation for the catabolism of the phenylurea herbicide linuron inVariovorax
Authors: Öztürk Başak , Werner Johannes , Meier-Kolthoff Jan P. , Bunk Boyke , Spröer Cathrin , Springael Dirk
Published: September 2019

Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of theVariovoraxgenus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full genome sequences of six linuron degradingVariovoraxstrains isolated from geographically distant locations were analyzed to acquire insight in the mechanisms of genetic adaptation towards linuron metabolism inVariovorax. Whole genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade withinVariovoraxand indicated their unlikely origin from a common ancestral linuron degrader. The linuron degraders differentiated from non-degraders by the presence of multiple plasmids of 20 to 839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed (i) high conservation and synteny and (ii) strain-dependent distribution among the different plasmids. All were bordered by IS1071elements forming composite transposon structures appointing IS1071as key for catabolic gene recruitment. Most of the strain carried at least one broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1Variovoraxstrains, despite their different geographical origin, made use of a limited genetic repertoire to acquire linuron biodegradation.

Importance

The genusVariovoraxand especially a clade of strains that phylogenetically separates from the majority ofVariovoraxspecies, appears to be a specialist in the biodegradation of the phenyl urea herbicide linuron. Horizontal gene transfer (HGT) likely played an essential role in the genetic adaptation of those strain to acquire the linuron catabolic genotype. However, we do not know the genetic repertoire involved in this adaptation both regarding catabolic gene functions as well as gene functions that promote HGT neither do we know how this varies between the different strains. These questions are addressed in this paper by analyzing the full genome sequences of six linuron degradingVariovoraxstrains. This knowledge is important for understanding the mechanisms that steer world-wide genetic adaptation in a particular species and this for a particular phenotypic trait as linuron biodegradation.
Ultra-low frequency neural entrainment to pain
Authors: Guo Y , Bufacchi RJ , Novembre G , Kilintari M , Moayedi M , Hu L , Iannetti GD
Published: September 2019

Nervous systems exploit regularities in the sensory environment to predict sensory input and adjust behavior, and thereby maximize fitness. Entrainment of neural oscillations allows retaining temporal regularities of sensory information, a prerequisite for prediction. Entrainment has been extensively described at the frequencies of periodic inputs most commonly present in visual and auditory landscapes (e.g. >1 Hz). An open question is whether neural entrainment also occurs for regularities at much longer timescales. Here we exploited the fact that the temporal dynamics of thermal stimuli in natural environment can unfold very slowly. We show that ultra-low frequency neural oscillations preserved a long-lasting trace of sensory information through neural entrainment to periodic thermo-nociceptive input as low as 0.1 Hz. Importantly, revealing the functional significance of this phenomenon, both power and phase of the entrainment predicted individual pain sensitivity. In contrast, periodic auditory input at the same ultra-low frequency did not entrain ultra-low frequency oscillations. These results demonstrate that a functionally-significant neural entrainment can occur at temporal scales far longer than those commonly explored. The non-supramodal nature of our results suggests that ultra-low frequency entrainment might be tuned to the temporal scale of the statistical regularities characteristic of different sensory modalities.
A Systematic Review of the Biomechanical Effects of Harness and Head-Collar use in Dogs
Authors: Blake S , Williams R , Ferro de Godoy R
Published: September 2019

The number of dogs in the UK is on the rise, as are canine sports involving the use of a harness to allow the dog to pull against an interface in the same way as a husky might pull a sled. Service dogs and those involved in essential work commonly wear a harness throughout their working lives, yet little is understood regarding the biomechanical impact of their use. This systematic review was conducted to review reported evidence of the biomechanical effects of harness and head collar (Halti) use in dogs.

Searches were applied covering 1910 to 2018 on the following databases: PubMed, Web of Science and Writtle Discovery.

Three publications were identified as suitable which were then critically evaluated using predefined criteria and ARRIVE based guidelines for bias assessment. Only one was considered to provide the most reliable data regarding the influence of harnesses on gait, whilst the remainder were considered to suffer a variety of issues including poor sample size, repeatability and study execution. The most appropriate study found that wearing a chest strap harness reduced shoulder extension in both walk and trot by up to 8° of movement, whilst a Y-shaped harness commonly marketed as non-restrictive reduced shoulder extension by up to 10° of movement, suggesting that the use of harness type restraints can affect canine gait, whereas no studies were found relating to the biomechanical effects of head-collar usage.
The expression of cannabinoid-related genes in multiple disease cell lines
Authors: Arlen Philip A. , Wu Xingzhu
Published: September 2019

The endocannabinoid system comprises a series of ligands and receptors that have putative roles in regulating physiological and cognitive processes such as pre- and post-natal development, appetite, pain sensation, mood, and memory. Besides the endocannabinoids, these endogenous receptors are also capable of mediating the pharmacological effects of phytocannabinoids, which are derived from the cannabis plant. We sought to interrogate a panel of cell lines, representative of multiple human diseases, to characterize their cannabinoid-mediating gene expression. We found all lines expressed one or more gene product that rendered the cell potentially responsive to cannabinoids. Moreover, the expression profiles differed between normal and cancerous cells, as well as between cells derived from the brain, pancreas, and skin. Taken together, given the presence of one or more of these mediating gene products, our findings suggest a potential therapeutic role for phytocannabinoids.
Effects of anesthetic tricaine on stress and reproductive aspects of South American silver catfish (Rhamdia quelen) male
Authors: dos Santos Teixeira Nathalia , Marques Lis Santos , Rodrigues Rômulo Batista , Gusso Darlan , Nunes Fossati Ana Amélia , Streit Danilo Pedro
Published: September 2019

Anesthesia is a common practice used in fish research and aquaculture. For both applications, it is important to understand anesthetics effects on the animal and tissues of interest to ensure the validity of data and to improve animal welfare. Captive fish production is only possible with artificial reproduction, and it is known that manipulation is a stressor stimulus in fish. The most common method of determining fish stress responses is measuring the circulating level of cortisol. Therefore, the purpose of this study was to evaluate the effects of different concentrations (100, 200, and 300 mg L-1) of the anesthetic tricaine methanesulfonate (MS-222) on cortisol levels and their influence on the sperm quality maintenance in Rhamdia quelen. After hormonal induction, 28 sexually mature males (average weight = 363.00 ± 71.24 g) were randomly distributed among treatments, and their semen and blood samples were collected. Anesthesia induction time, motility rate, sperm concentration and morphology, plasma cortisol levels, and reproductive hormones concentrations (testosterone, 17-α-hydroxyprogesterone, and estradiol) were evaluated. Anesthesia with 100 mg L-1 MS-222 presented a longer induction time than that with 200 and 300 mg L-1 MS-222. Sperm motility rate was significantly higher in the control than in the 300 mg L-1 treatment but did not differ among the control, 100, and 200 mg L-1 treatments. Estradiol level was significantly higher in non-anesthetized than in anesthetized fish, but plasma cortisol levels did not differ significantly between treatments (182.50 ± 42.03 ng mL-1). MS-222 anesthetizes fish by blocking the sodium channels, preventing the development of nerve action potentials. However, MS222 at concentrations of 100, 200, and 300 mg L-1 did not prevent stress in South American silver catfish males. In addition, its use did not maintain sperm quality, as it impaired motility and decreased levels of plasma estradiol.
Low concordance of short-term and long-term selection responses in experimentalDrosophilapopulations
Authors: Langmüller Anna Maria , Schlötterer Christian
Published: September 2019

Abstract

Experimental evolution is becoming a popular approach to study the genomic selection response of evolving populations. Computer simulation studies suggest that the accuracy of the signature increases with the duration of the experiment. Since some assumptions of the computer simulations may be violated, it is important to scrutinize the influence of the experimental duration with real data. Here, we use a highly replicated Evolve and Resequence study inDrosophila simulansto compare the selection targets inferred at different time points. At each time point, approximately the same number of SNPs deviates from neutral expectations, but only 10 % of the selected haplotype blocks identified from the full data set can be detected after 20 generations. Those haplotype blocks that emerge already after 20 generations differ from the others by being strongly selected at the beginning of the experiment and display a more parallel selection response. Consistent with previous computer simulations, our results demonstrate that only Evolve and Resequence experiments with a sufficient number of generations can characterize complex adaptive architectures.
Novel Universal Primers for Metabarcoding eDNA Surveys of Marine Mammals and Other Marine Vertebrates
Authors: Valsecchi Elena , Bylemans Jonas , Goodman Simon J. , Lombardi Roberto , Carr Ian , Castellano Laura , Galimberti Andrea , Galli Paolo
Published: September 2019

Metabarcoding studies using environmental DNA (eDNA) and high throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals have received less attention. Similarly, there have been few attempts to identify potentially ‘universal’ barcode loci which may be informative across multiple marine vertebrate Orders. Here we describe the design and validation of four new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. ‘In silico’ validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators.
Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis
Authors: Adams Taylor S. , Schupp Jonas C. , Poli Sergio , Ayaub Ehab A. , Neumark Nir , Ahangari Farida , Chu Sarah G. , Raby Benjamin A. , DeIuliis Giuseppe , Januszyk Michael , Duan Qiaonan , Arnett Heather A. , Siddiqui Asim , Washko George R. , Homer Robert , Yan Xiting , Rosas Ivan O. , Kaminski Naftali
Published: September 2019

We provide a single cell atlas of Idiopathic Pulmonary Fibrosis (IPF), a fatal interstitial lung disease, focusing on resident lung cell populations. By profiling 312,928 cells from 32 IPF, 29 healthy control and 18 chronic obstructive pulmonary disease (COPD) lungs, we demonstrate that IPF is characterized by changes in discrete subpopulations of cells in the three major parenchymal compartments: the epithelium, endothelium and stroma. Among epithelial cells, we identify a novel population of IPF enriched aberrant basaloid cells that co-express basal epithelial markers, mesenchymal markers, senescence markers, developmental transcription factors and are located at the edge of myofibroblast foci in the IPF lung. Among vascular endothelial cells in the in IPF lung parenchyma we identify an expanded cell population transcriptomically identical to vascular endothelial cells normally restricted to the bronchial circulation. We confirm the presence of both populations by immunohistochemistry and independent datasets. Among stromal cells we identify fibroblasts and myofibroblasts in both control and IPF lungs and leverage manifold-based algorithms diffusion maps and diffusion pseudotime to infer the origins of the activated IPF myofibroblast. Our work provides a comprehensive catalogue of the aberrant cellular transcriptional programs in IPF, demonstrates a new framework for analyzing complex disease with scRNAseq, and provides the largest lung disease single-cell atlas to date.
MeasuringC. elegansspatial foraging and food intake using bioluminescent bacteria
Authors: Ding Siyu Serena , Sarkisyan Karen S. , Brown Andre E. X.
Published: September 2019

For most animals, feeding includes two behaviours: foraging to find a food patch and food intake once a patch is found. The nematodeCaenorhabditis elegansis a useful model for studying the genetics of both behaviours. However, most methods of measuring feeding in worms quantify either foraging behaviour or food intake but not both. Imaging the depletion of fluorescently labelled bacteria provides information on both the distribution and amount of consumption, but even after patch exhaustion a prominent background signal remains, which complicates quantification. Here, we used a bioluminescentEscherichia colistrain to quantifyC. elegansfeeding. With light emission tightly coupled to active metabolism, only living bacteria are capable of bioluminescence so the signal is lost upon ingestion. We quantified the loss of bioluminescence using N2 reference worms andeat-2mutants, and found a nearly 100-fold increase in signal-to-background ratio and lower background compared to loss of fluorescence. We also quantified feeding using aggregatingnpr-1mutant worms. We found that groups ofnpr-1mutants first clear bacteria from each other before foraging collectively for more food; similarly, during high density swarming, only worms at the migrating front are in contact with bacteria. These results demonstrate the usefulness of bioluminescent bacteria for quantifying feeding and suggest a hygiene hypothesis for the function ofC. elegansaggregation and swarming.
Analysis of solvent-accessible voids and proton-coupled electron transfer of 2,6-bis(1H-imidazol-2-yl)pyridine and its hydrochloride
Authors: Guerra Renan B. , Huamaní Luis S. C. , Tenorio Juan C. , Guimarães Willian M. , Bonacin Juliano A. , Barboza Formiga André Luiz
Published: September 2019

The crystal structures of the solid form of solvated 2,6-bis(1H-imidazol-2-yl)pyridine (H2dimpy) trihydrate, C11H9N5·3H2O·[+solvent], I, and its hydrate hydrochloride salt 2-[6-(1H-imidazol-2-yl)pyridin-2-yl]-1H-imidazol-3-ium chloride trihydrate, C11H10N5
+·Cl−·3H2O, II, are reported and analysed in detail, along with potentiometric and spectrophotometric titrations for evaluation of the acid–base equilibria and proton-coupled electron-transfer reactions. Compound I crystallizes in the high-symmetry trigonal space group P3221 with an atypical formation of solvent-accessible voids, as a consequence of the 32 screw axis in the crystallographic c-axis direction, which are probably occupied by uncharacterized disordered solvent molecules. Additionally, the trihydrated chloride salt crystallizes in the conventional monoclinic space group P21/c without the formation of solvent-accessible voids. The acid–base equilibria of H2dimpy were studied by potentiometric and spectrophotometric titrations, and the results suggest the formation of H3dimpy+ (pK
a1 = 5.40) and H4dimpy2+ (pK
a2 = 3.98), with the electrochemical behaviour of these species showing two consecutive irreversible proton-coupled electron-transfer reactions. Density functional theory (DFT) calculations corroborate the interpretation of the experimental results and support the assignment of the electrochemical behaviour.
Crystal structure of a salt with a protonated sugar cation and a cobalt(II) complex anion: (GlcN–H, K)[Co(NCS)4]·2H2O
Authors: Peppel Tim , Detert Sabine M. L. , Vogel Christian , Köckerling Martin
Published: September 2019

The title compound, D-(+)-glucosammonium potassium tetrathiocyanatocobaltate(II) dihydrate, K(C6H14NO5)[Co(NCS)4]·2H2O or (GlcNH)(K)[Co(NCS)4]·2H2O, has been obtained as a side product of an incomplete salt metathesis reaction of D-(+)-glucosamine hydrochloride (GlcN·HCl) and K2[Co(NCS)4]. The asymmetric unit contains a D-(+)-glucosammonium cation, a potassium cation, a tetraisothiocyanatocobalt(II) complex anion and two water molecules. The water molecules coordinate to the potassium cation, which is further coordinated via three short K+...SCN− contacts involving three [Co(NCS)4]2− complex anions and via three O atoms of two D-(+)-glucosammonium cations, leading to an overall eightfold coordination around the potassium cation. Hydrogen-bonding interactions between the building blocks consolidate the three-dimensional arrangement.
An anti-interference detection algorithm for parking monitoring systems
Authors: Dong Ani , Zhang Zusheng , Chen Jiaming
Published: September 2019

Purpose

Magnetic sensors have recently been proposed for parking occupancy detection. However, there has adjacent interference problem, i.e. the magnetic signal is easy to be interfered by the vehicles which are parking on adjacent spaces. The purpose of this paper is to propose a sensing algorithm to eliminate the adjacent interference.

Design/methodology/approach

The magnetic signals are converted to the pattern representation sequences, and the similarity is calculated using the pattern distance. The detection algorithm includes two levels: local decision and data fusion. In the local decision level, the sampled signals can be divided into three classes: vacant, occupied and uncertain. Then a collaborative decision is used to fusion the signals which belong to the uncertain class for the second level.

Findings

An experiment system included 60 sensor nodes that were deployed on bay parking spaces. Experiment results show that the proposed algorithm has better detection accuracy than existing algorithms.

Originality/value

This paper proposes a data fusion algorithm to eliminate adjacent interference. To balance the energy consumption and detection accuracy, the algorithm includes two levels: local decision and data fusion. In most of cases, the local decision can obtain the accurate detection result. Only the signals that cannot be correctly detected at the local level need data fusion operation.
The well-being of the early career teacher: a review of the literature on the pivotal role of mentoring
Authors: Squires Vicki
Published: September 2019

Purpose

The purpose of this paper is to explore the extant literature with regard to the role of mentorship in promoting the well-being of early career teachers.

Design/methodology/approach

This paper was comprised of a review of the current literature. Key terms were used to identify initial sources. The search was narrowed further by using the Boolean operator AND to link key terms.

Findings

Much of the literature exploring mentorship and induction focuses on the formal structures and the targeted learning outcomes of the processes. However, the emotional and personal support afforded new teachers through the development of relationships with mentors is being recognized as contributing high value to the continued retention efforts. Although there are promising practices with regard to induction programs and formal mentorship arrangements in some schools, these practices are very scattered and may not even be equally well established within one school district.

Research limitations/implications

Implementation of models that are focused on personal and professional support of new teachers could provide an avenue of research examining teachers’ perceptions of well-being and resiliency. Longitudinal, pan-provincial and pan-national research is necessary for developing more support for systemic implementation of mentorship models.

Originality/value

While there is research identifying existing programs and induction models, this paper uses the lens of early career teacher well-being to point out promising practices and additional considerations for adopting a holistic approach to mentorship. This mentorship model may result in better personal and professional outcomes for new teachers.
Achieving automotive suppliers’ mass customization through modularity
Authors: Wu Qun , Liao Kun , Deng Xiaodong , Marsillac Erika
Published: September 2019

Purpose

Previous literature tends to combine postponement and modularity or view them as parallel factors to achieve mass customization (MC) while ignoring the sequence of a firm to design and implement operations and supply chain strategy. Based on a customer-oriented strategy and theories of organizational information processing theory, three-dimensional (3D) concurrent engineering and resource dependency, the purpose of this paper is to propose a sequential model reflecting the sequence of practices as well as an overview picture for a firm to achieve MC.

Design/methodology/approach

The model links three company antecedents – postponement orientation, operational alignment and information sharing, to three company supply chain practices – product and process modularity and supplier segmentation. These practices, in turn, lead to the company’s MC capabilities. The proposed model is tested with a data set collected from automotive suppliers in China and in the USA. Structural equation modeling is used to analyze the data and test the model.

Findings

The results suggest that, for suppliers to achieve MC, postponement orientation and operational alignment are vital antecedents. The results also reveal the important responsibility and role of information sharing practices in coordinating suppliers’ modularity practices.

Originality/value

This research provides three findings that are of value to both academicians and practitioners of supply chain management. First, this study originally proposed and empirically tested that a postponement orientation is an antecedent of product and process modularity and supplier segmentation to achieve MC in the automotive sector, contrary to the traditional view of parallel relationships for both. Second, it developed and verified measures of operational alignment and supplier segmentation for future research use. Third, the vital role of information sharing to coordinate internal and external supply chain practices to achieve MC is empirically supported.
In depth study of lead frame tape residuein quad flat non-leaded package
Authors: Nadaraja Shri Kumaran , Yap Boon Kar
Published: September 2019

Purpose

Lead frame tape is a crucial support for lead frames in the IC assembly process. The tape residue on the quad flat non-leaded (QFN) could result in low reliability and failure in electrical conductivity tests. The tape residue would affect overall performance of the chips and contribute to low pass yield. The purpose of this paper is to present an in-depth study of tape residue and factors that may affect it.

Design/methodology/approach

An experiment using lead frame and tapes from three manufacturers with two types of die bond adhesives, namely, die attach film (DAF) and wafer back coating (WBC), was conducted. Copper (Cu) wire bonding and die bonding performances were measured in terms of process capability, stitch bond strength and die attach strength.

Findings

Results showed that no tape residue was observed on the thermoplastic adhesive-based lead frames manufactured by Hitachi after the de-taping process because of the tape’s thermoplastic adhesive properties.

Originality/value

This paper studies the occurrence of tape residue and a viable solution for it through the correct process optimization and combination of semiconductor manufacturing materials. Factors that may affect tape residue have also been studied and further research can be done to explore other options in the future as an alternate solution.
Factors affecting political participation (Jordanian universities students' voting: field study 2017-2018)
Authors: Alelaimat Mohammad Soud
Published: September 2019

Purpose

This study aims to identify the factors affecting the political participation of Jordanian university students, especially their voting in national and local elections. The study examines the impact of gender, age, family income and regional affiliation that represent important social and economic factors affecting political participation on the voting of Jordanian university students.

Design/methodology/approach

Quantitative research method was used in this study. The study population contained three Jordanian universities representing the various segments of the Jordanian society: Al-Al Bayt University (Northern Region), Jordanian University (Central Region) and Mu'tah University (Southern Region). The study relied on a purposive sample of 900 students, 300 students per university (150 males and 150 females). The survey was conducted in the academic year 2018-2019. A questionnaire reviewed by two jurors (peer reviewers) was used to collect the data.

Findings

The study concluded that the gender, age, family income and regional affiliation factors affect the voting of Jordanian university students in national and local elections. The more the gender varies, the more the voting shifts in favor of males students. The more the age varies, the more the voting shifts in favor of older students. The more the family income varies, the more the voting shifts in favor of high-income students. The more the regional affiliation varies, the more the voting shifts in favor of Jordanians students.

Originality/value

This study is an approach to interpret the factors affecting voting of Jordanian university students, such as gender, age, family income and regional affiliation, which led to different voting in the national and local elections.