bluuebunny/crossref_metadata_2025 huggingface dataset:
Barriers to Utilization of Prescription Drug Monitoring Programs Among Prescribing Physicians and Advanced Practice Registered Nurses at Veterans Health Administration Facilities in Oregon
Authors: Mastarone Ginnifer L , Wyse Jessica J , Wilbur Eileen R , Morasco Benjamin J , Saha Somnath , Carlson Kathleen F
Published: October 2019

Objective

To identify barriers to using state prescription drug monitoring programs (PDMPs) among prescribing physicians and advanced practice registered nurses across a variety of Veterans Health Administration (VA) settings in Oregon.

Design

In-person and telephone-based qualitative interviews and user experience assessments conducted with 25 VA prescribers in 2018 probed barriers to use of state PDMPs.

Setting

VA health care facilities in Oregon.

Subjects

Physicians (N = 11) and advanced practice registered nurses (N = 14) who prescribed scheduled medications, provided care to patients receiving opioids, and used PDMPs in their clinical practice. Prescribers were stationed at VA medical centers (N = 10) and community-based outpatient clinics (N = 15); medical specialties included primary care (N = 10), mental health (N = 9), and emergency medicine (N = 6).

Methods

User experience was analyzed using descriptive statistics. Qualitative interviews were analyzed using conventional content analysis methodology.

Results

The majority of physicians (64%) and advanced practice registered nurses (79%) rated PDMPs as “useful.” However, participants identified both organizational and software design issues as barriers to their efficient use of PDMPs. Organizational barriers included time constraints, clinical team members without access, and lack of clarity regarding the priority of querying PDMPs relative to other pressing clinical tasks. Design barriers included difficulties entering or remembering passwords, unreadable data formats, time-consuming program navigation, and inability to access patient information across state lines.

Conclusions

Physicians and advanced practice registered nurses across diverse VA settings reported that PDMPs are an important tool and contribute to patient safety. However, issues regarding organizational processes and software design impede optimal use of these resources.
Effects of Student Physical Therapists on Clinical Instructor Productivity Across Settings in an Academic Medical Center
Authors: Apke Tonya L , Whalen Matthew , Buford John
Published: October 2019

Background

Clinical education is an integral component of physical therapy education. Both benefits and barriers exist in clinical education, but 1 commonly stated barrier includes the perception that students have a negative impact on clinical instructor productivity.

Objective

The purposes of this study were to evaluate the productivity of physical therapist clinical instructors in an academic medical center before, during, and after clinical education experiences, determine if there are differences in productivity during clinical education experiences across settings, and compare clinical instructor productivity with that of therapists who did not have a student during the same time frames.

Design

A retrospective design examined productivity across 3 years in acute care, inpatient rehabilitation, outpatient orthopedics, and outpatient neurology. Mean daily productivity was computed, normalized to an 8-hour day, and averaged for each week of the year. Data were analyzed using a repeated-measures ANOVA. Post-hoc comparisons were made within each setting to compare therapists with a student to those without. The Bonferonni-correction was used to control for multiple comparisons.

Results

Clinical instructor productivity was significantly increased in outpatient orthopedics and inpatient rehabilitation, and approached significance in outpatient neurology, but was not significant in acute care. The presence of a student made clinical instructors more productive but had no effect on the productivity of other therapists in that setting during the same time frame.

Limitations

We studied only 1 academic medical center and could not account for clinical instructor factors such as years of experience or student factors such as year in their program.

Conclusions

Our results indicate that having a student increases productivity of therapists in various settings. Future studies should examine the impact of clinical instructor experience and student characteristics and should expand to other settings.
ANGULAR DEPENDENCE OF TRACK-ETCH DETECTOR HARZLAS TD-1
Authors: Ambrožová Iva , Pachnerová Brabcová Kateřina , Shurshakov Vyacheslav A , Tolochek Raisa V , Kodaira Satoshi
Published: October 2019

Track-etched detectors are commonly used also for radiation monitoring onboard International Space Station. To be registered in track-etched detectors, the particle needs to meet several criteria—it must have linear energy transfer above the detection threshold and strike the detector’s surface under an angle higher than the so-called critical angle. Linear energy transfer is then estimated from calibration curve from the etch rate ratio V that is calculated from parameters of individual tracks appearing on the detector’s surface after chemical etching. It has been observed that V can depend on the incident angle and this dependence can vary for different detector materials, etching and evaluating conditions. To investigate angular dependence, detectors (Harzlas TD-1) were irradiated at HIMAC by several ions under angles from 0° to 90°. The correction accounting not only for critical angle but also for dependence of V on the incident angle is introduced and applied to spectra measured onboard International Space Station.
Dissociable roles of left and right temporoparietal junction in strategic competitive interaction
Authors: Ogawa Akitoshi , Kameda Tatsuya
Published: October 2019

Although many studies have shown that the temporoparietal junction (TPJ) is involved in inferring others’ beliefs, neural correlates of ‘second-order’ inferences (inferring another’s inference about one’s own belief) are still elusive. Here we report a functional magnetic resonance imaging experiment to examine the involvement of TPJ for second-order inferences. Participants played an economic game with three types of opponents: a human opponent outside the scanner, an artificial agent that followed a fixed probabilistic strategy according to a game-theoretic solution (FIX) and an artificial agent that adjusted its choices through a machine-learning algorithm (LRN). Participants’ choice behaviors against the human opponent and LRN were similar but remarkably different from those against FIX. The activation of the left TPJ (LTPJ) was correlated with choice behavior against the human opponent and LRN but not against FIX. The overall activity pattern of the LTPJ for the human opponent was also similar to that for LRN but not for FIX. In contrast, the right TPJ (RTPJ) showed higher activation for the human opponent than FIX and LRN. These results suggest that, while the RTPJ is associated with the perception of human agency, the LTPJ is involved in second-order inferences in strategic decision making.
Growth, performance, and carcass characteristics of feedlot Holstein steers fed ractopamine hydrochloride1
Authors: Lockard Cathy L , Richards Chris J , Lockard Caleb G , Youngers Maggie , Woolsoncroft Mariah A , Husz Taylor C , Wilson Blake K , Goad Carla L , Jackson Todd A , Step Douglas L , Bernhard Bryan C , Corbin Marilyn J , Krehbiel Clint R
Published: October 2019

Growth-promoting technologies such as implants, ionophores, and β-agonists improve feedlot performance, efficiency, and carcass characteristics of cattle. The objective of this experiment was to determine the effects of dose and duration of ractopamine hydrochloride (RH) on feedlot performance and carcass characteristics when fed to Holstein steers. A randomized complete block design was used with a 3 × 3 factorial arrangement of treatments with 3 RH doses (0, 300, or 400 mg∙steer−1∙d−1) fed for 3 durations (28, 35, or 42 d). Holstein steers (n = 855; initial body weight [BW] = 448 ± 37 kg) were blocked by BW and randomly allocated to 1 of 9 pens (15 blocks; 9 dose × duration treatment combinations) approximately 72 d before harvest. Weekly pen weights, chute temperament scores, and animal mobility were determined during the RH feeding period. At harvest, carcass data were collected on all steers, and tenderness was measured on steaks from 3 or 4 randomly selected steers from each pen and slice shear force (SSF) was determined on one steak selected from each side of the carcass after aging for 14 or 21 d. For feedlot performance, carcass characteristics, and SSF, no dose × duration interactions were observed (P ≥ 0.11). With increasing RH dose, average daily gain (ADG) and gain-to-feed ratio (G:F) increased linearly (P ≤ 0.01), whereas BW gain increased linearly with RH dose and duration (P ≤ 0.01). Hot carcass weight (P = 0.02) and longissimus muscle (LM) area (P ≤ 0.01) increased linearly with increasing RH dose. The percentage of carcasses in the USDA Yield Grade 2 category increased linearly (P ≤ 0.01) and percentage of carcasses in the USDA Yield Grade 4 category tended (P = 0.08) to decrease linearly as RH dose increased. In the 14-d aged steaks, the percentage of steaks with SSF ≤ 15.3 kg decreased linearly (P ≤ 0.01), whereas the percentage of steaks with ≥20.0 kg SSF increased linearly (P ≤ 0.01) with increasing RH dose. After 21-d aging, there was a tendency (P = 0.06) for a greater percentage of steaks from steers fed RH to have SSF ≥ 20.0 kg (2% of total steaks), but no difference (P ≥ 0.12) in the percentage of steaks with SSF ≤ 19.9 kg. Final chute temperament (P ≥ 0.45) and animal mobility (P ≥ 0.67) scores were not affected by feeding RH. Increasing the dose of RH (300 or 400 mg∙steer−1∙d−1) fed for 28 to 42 d before harvest increased ADG, G:F, hot carcass weight, and LM area when fed to Holstein steers with no negative effects on behavior or mobility. The percentage of steaks classified as not tender improved when steaks were aged for 21 d from steers treated with RH.
Current-year shoot hydraulic structure in two boreal conifers—implications of growth habit on water potential
Authors: Mäkelä Annikki , Grönlund Leila , Schiestl-Aalto Pauliina , Kalliokoski Tuomo , Hölttä Teemu
Published: October 2019

Metabolic scaling theory allows us to link plant hydraulic structure with metabolic rates in a quantitative framework. In this theoretical framework, we considered the hydraulic structure of current-year shoots in Pinus sylvestris and Picea abies, focusing on two properties unaccounted for by metabolic scaling theories: conifer needles are attached to the entire length of shoots, and the shoot as a terminal element does not display invariant properties. We measured shoot length and diameter as well as conduit diameter and density in two locations of 14 current-year non-leader shoots of pine and spruce saplings, and calculated conductivities of shoots from measured conduit properties. We evaluated scaling exponents for the hydraulic structure of shoots at the end of the water transport pathway from the data and applied the results to simulate water potential of shoots in the crown. Shoot shape was intermediate between cylindrical and paraboloid. Contrary to previous findings, we found that conduit diameter scaled with relative, not absolute, distance from the apex and absolute under-bark shoot diameter independently of species within the first-year shoots. Shoot hydraulic conductivity scaled with shoot diameter and hydraulic diameter. Larger shoots had higher hydraulic conductance. We further demonstrate by novel model calculations that ignoring foliage distribution along the hydraulic pathway overestimates water potential loss in shoots and branches and therefore overestimates related water stress effects. Scaling of hydraulic properties with shoot size enhances apical dominance and may contribute to the decline of whole-tree conductance in large trees.
Effectiveness and Safety of Hydroxyurea in the Treatment of Sickle Cell Anaemia Children in Jos, North Central Nigeria
Authors: Ofakunrin Akinyemi O D , Oguche Stephen , Adekola Kehinde , Okpe Edache S , Afolaranmi Tolulope O , Diaku-Akinwumi Ijeoma N , Zoakah Ayuba I , Sagay Atiene S
Published: October 2019

Background

Hydroxyurea has been shown to positively modify sickle cell disease pathogenesis, but its use is low among Nigerian sickle cell anaemia (SCA) patients because of effectiveness and safety concerns.

Methods

We conducted a quasi-experimental study to evaluate the effectiveness and safety of hydroxyurea in 54 SCA children aged 4–17 years. Clinical and haematological parameters were compared at baseline and 12 months after hydroxyurea therapy. The participants were monitored for adverse events. The parameters were compared using relative risk and Wilcoxon Signed-Rank Test.

Results

The number of subjects who had more than two episodes of painful crises reduced from 27 (50%) to 2 (2.7%) (p < 0.001), while those who had acute chest syndrome reduced from 6 (11.1%) to 0 (0.0%; p < 0.001). The risk of being transfused more than once was 0.11 times the risk in the 12 months period preceding therapy (95% CI = 0.02–0.85; p = 0.016). Similarly, the risk of hospital stay >7 days was 0.08 times the risk at the baseline (95% CI = 0.02–0.24; p < 0.0001). The median haematocrit and percentage foetal haemoglobin increased from 26 to 28% and 7.8 to 14%, respectively (p < 0.0001). A dose-dependent but reversible leucopenia was observed among six children (11.1%), otherwise, hydroxyurea was safe in the study population.

Conclusion

Hydroxyurea is effective and safe in SCA children in Jos, Nigeria. The findings could strengthen educational programme aimed at improving the utilization of hydroxyurea among SCA children.
Risk-Stratification of Children Presenting to Ambulatory Paediatrics with First-Onset Seizures: Should We Order an Urgent CT Brain?
Authors: Brugman Jaanri , Solomons Regan Shane , Lombard Carl , Redfern Andrew , Du Plessis Anne-Marie
Published: October 2019

Introduction

A computed tomography (CT) brain scan is an often-utilised emergency department imaging modality to detect emergent intra-cranial pathology in a child with a first seizure. Identifying children at low risk of having a clinically significant intra-cranial abnormality could prevent unnecessary radiation exposure and contrast/sedation-related risks.

Objectives

To identify clinical variables which could predict clinically significant CT brain abnormalities and use recursive partitioning analysis to define a low-risk group of children in whom emergent CT brain can be deferred.

Methods

Retrospective cross-sectional review of 468 children who underwent emergent CT brain after presenting to a low- and middle-income paediatric emergency department following first seizure.

Results

In total 133/468 (28.4%) of CT brain scans had clinically significant abnormalities. Failure to return to neurological baseline and focal neurological deficit persisting >36 h had statistical significance in a multiple regression analysis. Recursive partitioning analysis, applied to a subgroup without suspected tuberculous meningitis (n = 414), classified 153 children aged between 6 months and 5 years, who had a normal neurological baseline, had returned to baseline post-seizure, and were not in status epilepticus, as non-clinically significant scans and 98% were correctly classified.

Conclusion

Our study re-inforces the American Academy of Neurology recommendation that children with persistent post-ictal abnormal neurological status and/or post-ictal focal deficit be prioritised for emergent CT brain. Having excluded children with suspected tuberculous meningitis, the remaining subgroup aged 6 months to 5 years presenting with a non-status first seizure, normal neurological baseline and return to baseline post-seizure, are at very low risk of having a clinically significant CT brain abnormality.
Reduction in Perinatal Mortality after Implementation of HBB Training at a District Hospital in Mali
Authors: Innerdal M , Simaga I , Diall H , Eielsen M , Niermeyer S , Eielsen O , Saugstad O D
Published: October 2019

Background

Mali has a high neonatal mortality rate of 38/1000 live births; in addition the fresh stillbirth rate (FSR) is 23/1000 births and of these one-third are caused by intrapartum events.

Objectives

The aims are to evaluate the effect of helping babies breathe (HBB) on mortality rate at a district hospital in Kati district, Mali.

Methods

HBB first edition was implemented in April 2016. One year later the birth attendants were trained in HBB second edition and started frequent repetition training. This is a before and after study comparing the perinatal mortality during the period before HBB training with the period after HBB training, the period after HBB first edition and the period after HBB second edition. Perinatal mortality is defined as FSR plus neonatal deaths in the first 24 h of life.

Results

There was a significant reduction in perinatal mortality rate (PMR) between the period before and after HBB training, from 21.7/1000 births to 6.0/1000 live births; RR 0.27, (95% CI 0.19–0.41; p < 0.0001). Very early neonatal mortality rate (24 h) decreased significantly from 6.3/1000 to 0.8/1000 live births; RR 0.12 (95% CI 0.05–0.33; p = 0.0006). FSR decreased from 15.7/1000 to 5.3/1000, RR 0.33 (95% CI 0.22–0.52; p < 0.0001). No further reduction occurred after introducing the HBB second edition.

Conclusion

HBB may be effective in a local first-level referral hospital in Mali.
Efficacy of Natamycin Against Gray Mold of Stored Mandarin Fruit Caused by Isolates of Botrytis cinerea With Multiple Fungicide Resistance
Authors: Saito S. , Wang F. , Xiao C. L.
Published: October 2019

Gray mold caused by Botrytis cinerea is an emerging postharvest disease of mandarin fruit in California. Management of postharvest diseases of mandarins relies on postharvest fungicides; however, multiple resistance to fungicides of different modes of action is common in B. cinerea populations from mandarin, leading to their failure to control decay. Natamycin is commonly used in the food industry as an additive, and it has been registered as a biofungicide for postharvest use on citrus and some other fruits. Sensitivity to natamycin of 64 isolates of B. cinerea from decayed mandarin fruit with known resistance phenotypes to other citrus postharvest fungicides (azoxystrobin, fludioxonil, pyrimethanil, and thiabendazole) was tested. Effective concentrations of natamycin to cause a 50% reduction relative to the control for conidial germination were from 0.324 to 0.567 µg/ml (mean of 0.444 µg/ml), and those for mycelial growth were 1.021 to 2.007 µg/ml (mean of 1.578 µg/ml). Minimum inhibitory concentrations where no fungal growth was present were 0.7 to 1.0 µg/ml for conidial germination and 5.0 to 10.0 µg/ml for mycelial growth. No cross-resistance between natamycin and other citrus postharvest fungicides was detected. Decay control efficacy tests with natamycin were conducted on mandarin fruit inoculated with B. cinerea isolates exhibiting five different fungicide resistance phenotypes, and natamycin significantly reduced incidence and lesion size of gray mold on fruit, regardless of fungicide resistance phenotypes. Natamycin has the potential to be an effective tool for integration into postharvest fungicide programs to control gray mold and manage B. cinerea isolates resistant to fungicides with other modes of action.
Quantitative PCR Assays Developed for Diaporthe helianthi and Diaporthe gulyae for Phomopsis Stem Canker Diagnosis and Germplasm Screening in Sunflower (Helianthus annuus)
Authors: Elverson Taylor R. , Kontz Brian J. , Markell Samuel G. , Harveson Robert M. , Mathew Febina M.
Published: October 2019

Phomopsis stem canker of sunflower is caused by two fungal pathogens, Diaporthe helianthi and Diaporthe gulyae, in the United States. In this study, two quantitative PCR (qPCR) assays were developed to detect and quantify D. helianthi and D. gulyae in sunflower. The two assays differentiated the two fungi from each other, other species of the genus Diaporthe, and pathogens, and they have high efficiency (>90%). The qPCR assays detected the two pathogens on plant samples exhibiting Phomopsis stem canker symptoms sampled from commercial sunflower fields in Minnesota, Nebraska, North Dakota, and South Dakota. Furthermore, the assays were used to screen cultivated sunflower accessions for resistance to D. helianthi and D. gulyae. The disease severity index (DSI) of the accessions significantly correlated (P < 0.0001) with the amount of pathogen DNA from the qPCR assays. The qPCR assays identified PI664232 and PI561918 to be significantly less susceptible (P ≤ 0.05) to D. helianthi and D. gulyae, respectively, when compared with the susceptible check cultivar HA 288, and this was in agreement with the DSI. These results suggest that the qPCR assays for D. helianthi and D. gulyae can be used as a reliable tool to diagnose Phomopsis stem canker and screen sunflower germplasm for disease resistance.
Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization
Authors: Savin Cyril , Criscuolo Alexis , Guglielmini Julien , Le Guern Anne-Sophie , Carniel Elisabeth , Pizarro-Cerdá Javier , Brisse Sylvain
Published: October 2019

The genus

Yersinia

comprises species that differ widely in their pathogenic potential and public-health significance. Yersinia pestis is responsible for plague, while Yersinia enterocolitica is a prominent enteropathogen. Strains within some species, including Y. enterocolitica, also vary in their pathogenic properties. Phenotypic identification of

Yersinia

species is time-consuming, labour-intensive and may lead to incorrect identifications. Here, we developed a method to automatically identify and subtype all

Yersinia

isolates from their genomic sequence. A phylogenetic analysis of

Yersinia

isolates based on a core subset of 500 shared genes clearly demarcated all existing

Yersinia

species and uncovered novel, yet undefined

Yersinia

taxa. An automated taxonomic assignment procedure was developed using species-specific thresholds based on core-genome multilocus sequence typing (cgMLST). The performance of this method was assessed on 1843 isolates prospectively collected by the French National Surveillance System and analysed in parallel using phenotypic reference methods, leading to nearly complete (1814; 98.4 %) agreement at species and infra-specific (biotype and serotype) levels. For 29 isolates, incorrect phenotypic assignments resulted from atypical biochemical characteristics or lack of phenotypic resolution. To provide an identification tool, a database of cgMLST profiles and reference taxonomic information has been made publicly accessible (https://bigsdb.pasteur.fr/yersinia). Genomic sequencing-based identification and subtyping of any

Yersinia

is a powerful and reliable novel approach to define the pathogenic potential of isolates of this medically important genus.
Identification of functionally connected multi-omic biomarkers for Alzheimer’s Disease using modularity-constrained Lasso
Authors: Xie Linhui , Varathan Pradeep , Nho Kwangsik , Saykin Andrew J. , Salama Paul , Yan Jingwen
Published: October 2019

In the past decade, a large number of genetic biomarkers have been discovered through large-scale genome wide association studies (GWASs) in Alzheimer’s disease (AD), such asAPOE, TOMM40andCLU. Despite this significant progress, existing genetic findings are largely passengers not directly involved in the driver events, which presents challenges for replication and translation into targetable mechanisms. In this paper, leveraging the protein interaction network, we proposed a modularity-constrained Lasso model to jointly analyze the genotype, gene expression and protein expression data. With a prior network capturing the functional relationship between SNPs, genes and proteins, the newly introduced penalty term maximizes the global modularity of the subnetwork involving selected markers and encourages the selection of multi-omic markers with dense functional connectivity, instead of individual markers. We applied this new model to the real data in ROS/MAP cohort for discovery of biomarkers related to cognitive performance. A functionally connected subnetwork involving 276 multi-omic biomarkers, including SNPs, genes and proteins, were identified to bear predictive power. Within this subnetwork, multiple trans-omic paths from SNPs to genes and then proteins were observed, suggesting that cognitive performance can be potentially affected by the genetic mutations due to their cascade effect on the expression of downstream genes and proteins.
The RNA export factor Mex67 functions as a mobile nucleoporin
Authors: Derrer Carina Patrizia , Mancini Roberta , Vallotton Pascal , Huet Sébastien , Weis Karsten , Dultz Elisa
Published: October 2019

The RNA export factor Mex67 is essential for the transport of mRNA through the nuclear pore complex (NPC) in yeast, but the molecular mechanism of this export process remains poorly understood. Here, we use quantitative fluorescence micro-scopy techniques in live budding yeast cells to investigate how Mex67 facilitates mRNA export. We show that Mex67 exhibits little interaction with mRNA in the nucleus and localizes to the NPC independently of mRNA, occupying a set of binding sites offered by FG repeats in the NPC. The ATPase Dbp5, which is thought to remove Mex67 from transcripts, does not affect the interaction of Mex67 with the NPC. Strikingly, we find that the essential function of Mex67 is spatially restricted to the NPC since a fusion of Mex67 to the nucleoporin Nup116 rescues a deletion of MEX67. Thus, Mex67 functions as a mobile nuclear pore component, which receives mRNA export substrates in the central channel of the NPC to facilitate their translocation to the cytoplasm.
β-arrestin-dependent ERK signaling positively correlates with reduced anxiety-like and conditioned fear-related behavior in mice
Authors: Ko Mee Jung , Chiang Terrance , Mukadam Arbaaz A. , Mulia Grace E. , Gutridge Anna M. , Lin Angel , Chester Julia A. , van Rijn Richard M.
Published: October 2019

Exposure to anxiety- or fear-invoking stimuli initiates a convergence of executive actions orchestrated by multiple proteins and neurotransmitters across the brain. Dozens of G protein-coupled receptors (GPCRs) have been linked to regulation of fear and anxiety. GPCR signaling involves canonical G protein pathways but may also engage downstream kinases and effectors through β-arrestin scaffolds. Here, we investigate whether β-arrestin signaling can regulate anxiety-like and fear-related behavior. Using the δ-opioid receptor (δOR) as a model GPCR, we found that β-arrestin 2-dependent activation of extracellular signal–regulated kinases (ERK1/2) in the dorsal hippocampus and the amygdala are critical for δOR agonist-induced anxiolytic-like effects. In contrast, G protein-mediated δOR signaling was associated with decreased ERK1/2 activity and increased fear-related behavior. Our results also indicate unique contributions for β-arrestin isoforms in modulation of anxiety-like and fear-related behavior. Overall, our findings highlight the significance of non-canonical β-arrestin signaling in the regulation of emotions.

One sentence summary

Using pharmacological and genetic strategies, we reveal the importance of non-canonical β-arrestin-mediated G protein-coupled receptor signaling in anxiety-like behaviors.
Antibody-free enzyme-assisted chemical labeling for detection of transcriptome-wideN6-methyladenosine
Authors: Wang Ye , Xiao Yu , Dong Shunqing , Yu Qiong , Jia Guifang
Published: October 2019

The inert chemical property of RNA modificationN6-methyladenosine (m6A) makes it very challenging to detect, and all of the transcriptome-wide m6A detection methods rely on m6A-antibody immunoprecipitation. However, their results are dependent on the quality and specificity of antibodies. Although the endoribonuclease-based single-base m6A sequencing is antibody-free, it maps only 16~25% sites. Here, we present an antibody-free, FTO-assisted chemical labeling method termed m6A-SEAL for m6A detection. We applied m6A-SEAL to profile m6A landscapes in human and plant, which had good overlaps with antibody-based results and displayed the known m6A distribution features in transcriptome. Comparison with all available m6A sequencing methods and specific m6A sites validation by SELECT, we demonstrated that m6A-SEAL has good sensitivity, specificity, and reliability for transcriptome-wide detection of m6A. Given its tagging ability and FTO’s oxidation property, m6A-SEAL enables many applications like enrichment, imaging, and sequencing techniques to drive future functional studies of m6A and other modifications.
Different preference functions act in unison: mate choice and risk-taking behaviour in the Atlantic molly (Poecilia mexicana)
Authors: Sommer-Trembo Carolin , Schreier Michael , Plath Martin
Published: October 2019

Consistent individual differences in behaviour (animal personality) are widespread throughout the Animal Kingdom. This includes variation in risk-taking versus risk-averse behavioural tendencies. Variation in several personality dimensions is associated with distinct fitness consequences and thus, may become a target of natural and/or sexual selection. However, the link between animal personality and mate choice—as a major component of sexual selection—remains understudied. We asked (1) whether females and males of the livebearing fish Poecilia mexicana prefer risk-taking mating partners (directional mating preference), (2) or if their preferences are dependent on the choosing individual’s own personality type (assortative mating). We characterized each test subject for its risk-taking behaviour, assessed as the time to emerge from shelter and enter an unknown area. In dichotomous association preference tests, we offered two potential mating partners that differed in risk-taking behaviour but were matched for other phenotypic traits (body size, shape, and colouration). Females, but not males, exhibited a strong directional preference for risk-taking over risk-averse mating partners. At the same time, the strength of females’ preferences correlated positively with their own risk-taking scores. Our study is the first to demonstrate that a strong overall preference for risk-taking mating partners does not preclude effects of choosing individuals’ own personality type on (subtle) individual variation in mating preferences. More generally, two different preferences functions appear to interact to determine the outcome of individual mate choice decisions.
LAMBDR: Long-range amplification and Nanopore sequencing of theMycobacterium bovis direct-repeat region. A novel method for in-silico spoligotyping ofM. bovisdirectly from badger faeces
Authors: James R.S. , Travis E.R. , Millard A. D. , Hewlett P.C. , Kravar-Garde L. , Wellington E.M.
Published: October 2019

The environment is an overlooked source ofMycobacterium bovis, the causative agent of bovine TB. Long read, end to end sequencing of variable repeat regions across theM. bovisgenome was evaluated as a method of acquiring rapid strain level resolution directly from environmental samples. Eight samples ofM. bovis, two BCG strains (Danish and Pasteur), and a singleM. tuberculosistype culture (NCTC 13144) were used to generate data for this method. Long range PCR amplification of the direct repeat region was used to synthesize ∼5kb template DNA for onward sequence analysis. This has permitted culture independent identification ofM. bovisspoligotypes present in the environment. Sequence level analysis of the direct repeat region showed that spoligotyping may underestimate strain diversity due to the inability to identify both SNPs and primer binding mutations using a biotinylated hybridisation approach.
Molecular and Behavioral Effects of Infant Maltreatment across Generations in Rhesus Monkeys
Authors: Klengel Torsten , Morin Elyse L. , Howell Brittany R. , Bramlett Sara , Guzman Dora , Meyer Jerrold S. , Ressler Kerry J. , Sanchez M. Mar
Published: October 2019

Childhood maltreatment is among the most robust risk factors for subsequent psychiatric and medical disorders, and data in humans and rodents suggest that effects of adverse childhood experiences may be transmitted across generations. Recent indications for biological processes underlying this transfer of experiential effects are intriguing; yet, their relevance in primates is inconclusive due to limitations of current studies. In this study, we bridge research in rodent models and humans with a natural non-human primate model on intergenerational effects of childhood maltreatment. Using a unique, well-controlled, randomized cross-fostering design in rhesus monkeys, we test the influence of ancestral maltreatment on molecular, neuroendocrine and behavioral outcomes in offspring, and show that childhood maltreatment results in transmission of information to the subsequent generation independent of behavioral transmission. We further demonstrate differences in the offspring longitudinal DNA methylation profile of theFKBP5gene, an important regulator of the hypothalamus-pituitary-adrenal axis in offspring of the maltreatment lineage compared to the control lineage. Finally, we show that differences inFKBP5methylation have functional effects on molecular, neuroendocrine and behavioral outcomes in offspring of the maltreatment ancestral line, even if the infants were never exposed to maltreatment nor interacted with their exposed ancestors. Although the molecular mechanism underlying our observations remains unknown, our data point to a potential germline-dependent effect. In summary, our data suggest that history of maltreatment in primates can induce molecular and behavioral changes in a subsequent generation independent of behavioral transmission that may influence risk for mental and physical diseases across generations.
CALX-CBD1 Ca2+-binding cooperativity studied by NMR spectroscopy and ITC with Bayesian statistics
Authors: Cardoso M. V. C. , Rivera J. D. , Vitale P. M. , Degenhardt M. F. S. , Abiko L.A. , Oliveira C. L. P. , Salinas R. K.
Published: October 2019

The Na+/Ca2+ exchanger of Drosophila melanogaster, CALX, is the main Ca2+-extrusion mechanism in olfactory sensory neurons and photoreceptor cells. Na+/Ca2+ exchangers have two Ca2+ sensor domains, CBD1 and CBD2. In contrast to the mammalian homologues, CALX is inhibited by Ca2+-binding to CALX-CBD1, while CALX-CBD2 does not bind Ca2+ at physiological concentrations. CALX-CBD1 consists of a β-sandwich and displays four Ca2+ binding sites at the tip of the domain. In this study, we used NMR spectroscopy and isothermal titration calorimetry (ITC) to investigate the cooperativity of Ca2+-binding to CALX-CBD1. We observed that this domain binds Ca2+ in the slow exchange regime at the NMR chemical shift time scale. Ca2+-binding restricts the dynamics in the Ca2+-binding region. Experiments of 15N CEST and 15N R2 dispersion allowed the determination of Ca2+ dissociation rates (≈ 20 s−1). NMR titration curves of residues in the Ca2+-binding region were sigmoidal due to the contribution of chemical exchange to transverse magnetization relaxation rates, R2. Hence, a novel approach to analyze NMR titration curves was proposed. Ca2+-binding cooperativity was examined assuming two different stoichiometric binding models and using a Bayesian approach for data analysis. Fittings of NMR and ITC binding curves to the Hill model yielded nHill = 2.9 − 3.1, near maximum cooperativity (nHill = 4). By assuming a stepwise model to interpret the ITC data, we found that the probability of binding from 2 up to 4 Ca2+ is at least three orders of magnitude higher than that of binding a single Ca2+. Hence, four Ca2+ ions bind almost simultaneously to CALX-CBD1. Cooperative Ca2+-binding is key to enable this exchanger to efficiently respond to changes in the intracellular Ca2+-concentration in sensory neuronal cells.

SIGNIFICANCE

CALX-CBD1 is the Ca2+-sensor domain of the Na+/Ca2+ exchanger of Drosophila melanogaster. It consists of a β-sandwich, and contains four Ca2+ binding sites at the distal loops. In this study, we examined the cooperative binding of four Ca2+ ions to CALX-CBD1 using NMR spectroscopy and isothermal titration calorimetry (ITC) experiments. NMR and ITC data were analyzed using the framework of the binding polynomial formalism and Bayesian statistics. A novel approach to analyze NMR titration data in the slow exchange regime was proposed. These results support the view that CALX-CBD1 binds four Ca2+ with high cooperativity. The significant ligand binding cooperativity exhibited by this domain is determinant for the efficient allosteric regulation of this exchanger by intracellular Ca2+.
Hunting strategies and the lateral line of Astyanax mexicanus larva
Authors: Yoffe Marina , Patel Kush , Palia Eric , Kolawole Samuel , Streets Amy , Haspel Gal , Soares Daphne
Published: October 2019

The lateral line is the primary modality fish use to create a hydrodynamic image of their environment. These images contribute to a variety of behaviors, from rheotaxis to escape responses. Here we discern the contributions of visual and lateral line modalities in hunting behavior of larvae that have developed under different photic conditions. In particular, cave animals have a hypertrophied sense of mechanosensation, and we studied the common animal model cavefish Astyanax mexicanus and its closest related surface relative. We raised larvae in a diurnal light-dark regimen and in complete darkness. We then examined the distribution of neuromasts in their lateral lines, and their hunting performance in light and dark conditions, with and without the contribution of the lateral line. We report that all larva depend on the lateral line for success in hunting and that surface fish raised in the dark have a greater dependency on the lateral line,
Regulatory Feedbacks on Receptor and Non-receptor Synthesis for Robust Signaling
Authors: Lander A.D. , Nie Q. , Sanchez-Tapia C. , Simonyan A. , Wan F.Y.M.
Published: October 2019

Elaborate feedback regulatory processes are thought to make biological developments robust, i.e., resistant to changes induced by genetic or environmental perturbations. How this might be done is still not completely understood. Previous numerical simulations on reaction-diffusion models of Dpp gradients in Drosophila wing imaginal disc showed that feedback (of the Hill’s function type) on (signaling) receptors and/or non-(signaling) receptors are of limited effectiveness in promoting robustness. Spatial nonuniformity of the feedback processes is thought to lead to serious shape distortion and a principal cause for ineffectiveness. Through mathematical modeling of a spatially uniform nonlocal feedback mechanism, the present paper provides a theoretical support of these observations. More significantly, the new approach also enables us to uncover in this paper a new, theory-based multi-feedback instrument for broadly effective promotion of robust signaling gradients.
A phage display approach to identify highly selective covalent binders
Authors: Chen Shiyu , Bogyo Matthew
Published: October 2019

Molecules that bind macromolecular targets through direct covalent modification have found widespread applications as activity-based probes (ABPs) and as irreversible drugs. Covalent binders can be used to dynamically monitor the activity of enzymes in complex cellular environments, identify targets and induce permanent binding/inhibition of therapeutically important biomolecules. However, the general reactivity of the electrophiles needed for covalent bond formation makes control of selectivity difficult. There is currently no rapid, robust and unbiased screening method to identify new classes of covalent binding ligands from highly diverse pools of candidate molecules. Here we describe the development of a phage display method to screen for highly selective covalent binding ligands. This approach makes use of a reactive linker to form cyclic peptides on the phage surface while simultaneously introducing an electrophilic ‘warhead’ to covalently react with a nucleophile on the target. Using this approach, we identified cyclic peptides that selectively and irreversibly inhibited a cysteine protease with nanomolar potency, exceptional specificity and increased serum stability compared to a linear peptide containing the same electrophile. This approach should enable rapid, unbiased screening to identify new classes of highly selective covalent binding ligands for diverse molecular targets.
Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis
Authors: Russkikh N. , Antonets D. , Shtokalo D. , Makarov A. , Vyatkin Y. , Zakharov A. , Terentyev E.
Published: October 2019

Motivation

The transcriptomic data is being frequently used in the research of biomarker genes of different diseases and biological states. The most common tasks there are data harmonization and treatment outcome prediction. Both of them can be addressed via the style transfer approach. Either technical factors or any biological details about the samples which we would like to control (gender, biological state, treatment etc.) can be used as style components.

Results

The proposed style transfer solution is based on Conditional Variational Autoencoders, Y-Autoencoders and adversarial feature decomposition. In order to quantitatively measure the quality of the style transfer, neural network classifiers which predict the style and semantics after training on real expression were used. Comparison with several existing style-transfer based approaches shows that proposed model has the highest style prediction accuracy on all considered datasets while having comparable or the best semantics prediction accuracy.

Availability

https://github.com/NRshka/stvae-source

Contact

antonec@novel-soft.com

Supplementary information

FigShare.com (https://dx.doi.org/10.6084/m9.figshare.9925115)
Mechanism of manganese dysregulation of dopamine neuronal activity
Authors: Lin Min , Colon-Perez Luis M. , Sambo Danielle O. , Miller Douglas R. , Lebowitz Joseph J. , Jimenez-Rondan Felix , Cousins Robert J. , Horenstein Nicole , Aydemir Tolunay Beker , Febo Marcelo , Khoshbouei Habibeh
Published: October 2019

Manganese exposure produces Parkinson’s-like neurological symptoms, suggesting a selective dysregulation of dopamine transmission. It is unknown, however, how manganese accumulates in dopaminergic brain regions or how it regulates the activity of dopamine neurons. Ourin vivostudies suggest manganese accumulates in dopamine neurons of the ventral tegmental area and substantia nigra via nifedipine-sensitive Ca2+channels. Manganese produces a Ca2+channel-mediated current which increases neurotransmitter release and rhythmic firing activity of dopamine neurons. These increases are prevented by blockade of Ca2+channels and depend on downstream recruitment of Ca2+-activated potassium channels to the plasma membrane. These findings demonstrate the mechanism of manganese-induced dysfunction of dopamine neurons, and reveal a potential therapeutic target to attenuate manganese-induced impairment of dopamine transmission.

Significance Statement

Manganese is a trace element critical to many physiological processes. Overexposure to manganese is an environmental risk factor for neurological disorders such as a Parkinson’s disease-like syndrome known as manganism. We found manganese dose-dependently increased the excitability of dopamine neurons, decreased the amplitude of action potentials, and narrowed action potential width. Blockade of Ca2+channels prevented these effects as well as manganese accumulation in the mouse midbrainin vivo. Our data provide a potential mechanism for manganese-regulation of dopaminergic neurons.
A strategy to incorporate prior knowledge into correlation network cutoff selection
Authors: Benedetti Elisa , Pučić-Baković Maja , Keser Toma , Gerstner Nathalie , Büyüközkan Mustafa , Štambuk Tamara , Selman Maurice H.J. , Rudan Igor , Polašek Ozren , Hayward Caroline , Al-Amin Hassen , Suhre Karsten , Kastenmüller Gabi , Lauc Gordan , Krumsiek Jan
Published: October 2019

Correlation networks are commonly used to statistically extract biological interactions between omics markers. Network edge selection is typically based on the significance of the underlying correlation coefficients. A statistical cutoff, however, is not guaranteed to capture biological reality, and heavily depends on dataset properties such as sample size. We here propose an alternative, innovative approach to address the problem of network reconstruction. Specifically, we developed a cutoff selection algorithm that maximizes the agreement to a given ground truth. We first evaluate the approach on IgG glycomics data, for which the biochemical pathway is known and well-characterized. The optimal network outperforms networks obtained with statistical cutoffs and is robust with respect to sample size. Importantly, we can show that even in the case of incomplete or incorrect prior knowledge, the optimal network is close to the true optimum. We then demonstrate the generalizability of the approach on an untargeted metabolomics and a transcriptomics dataset from The Cancer Genome Atlas (TCGA). For the transcriptomics case, we demonstrate that the optimized network is superior to statistical networks in systematically retrieving interactions that were not included in the biological reference used for the optimization. Overall, this paper shows that using prior information for correlation network inference is superior to using regular statistical cutoffs, even if the prior information is incomplete or partially inaccurate.
Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-β signaling
Authors: Aragón Eric , Wang Qiong , Zou Yilong , Morgani Sophie M. , Ruiz Lidia , Kaczmarska Zuzanna , Su Jie , Torner Carles , Tian Lin , Hu Jing , Shu Weiping , Agrawal Saloni , Gomes Tiago , Márquez José A. , Hadjantonakis Anna-Katerina , Macias Maria J. , Massagué Joan
Published: October 2019

TGF-β receptors phosphorylate SMAD2 and SMAD3 transcription factors, which then form heterotrimeric complexes with SMAD4 and cooperate with context-specific transcription factors to activate target genes. Here we provide biochemical and structural evidence showing that binding of SMAD2 to DNA depends on the conformation of the E3 insert, a structural element unique to SMAD2 and previously thought to render SMAD2 unable to bind DNA. Based on this finding, we further delineate TGF-β signal transduction by defining distinct roles for SMAD2 and SMAD3 with the forkhead pioneer factor FOXH1 as a partner in the regulation of differentiation genes in mouse mesendoderm precursors. FOXH1 is prebound to target sites in these loci and recruits SMAD3 independently of TGF-β signals, whereas SMAD2 remains predominantly cytoplasmic in the basal state and set to bind SMAD4 and join SMAD3:FOXH1 at target promoters in response to Nodal TGF-β signals. The results support a model in which signal-independent binding of SMAD3 and FOXH1 prime mesendoderm differentiation gene promoters for activation, and signal-driven SMAD2:SMAD4 binds to promoters that are preloaded with SMAD3:FOXH1 to activate transcription.