bluuebunny/crossref_metadata_2025 huggingface dataset:
What health records data are required for accurate prediction of suicidal behavior?
Authors: Simon Gregory E , Shortreed Susan M , Johnson Eric , Rossom Rebecca C , Lynch Frances L , Ziebell Rebecca , Penfold and Robert B
Published: July 2019

Objective

The study sought to evaluate how availability of different types of health records data affect the accuracy of machine learning models predicting suicidal behavior.

Materials and Methods

Records from 7 large health systems identified 19 061 056 outpatient visits to mental health specialty or general medical providers between 2009 and 2015. Machine learning models (logistic regression with penalized LASSO [least absolute shrinkage and selection operator] variable selection) were developed to predict suicide death (n = 1240) or probable suicide attempt (n = 24 133) in the following 90 days. Base models were used only historical insurance claims data and were then augmented with data regarding sociodemographic characteristics (race, ethnicity, and neighborhood characteristics), past patient-reported outcome questionnaires from electronic health records, and data (diagnoses and questionnaires) recorded during the visit.

Results

For prediction of any attempt following mental health specialty visits, a model limited to historical insurance claims data performed approximately as well (C-statistic 0.843) as a model using all available data (C-statistic 0.850). For prediction of suicide attempt following a general medical visit, addition of data recorded during the visit yielded a meaningful improvement over a model using all data up to the prior day (C-statistic 0.853 vs 0.838).

Discussion

Results may not generalize to setting with less comprehensive data or different patterns of care. Even the poorest-performing models were superior to brief self-report questionnaires or traditional clinical assessment.

Conclusions

Implementation of suicide risk prediction models in mental health specialty settings may be less technically demanding than expected. In general medical settings, however, delivery of optimal risk predictions at the point of care may require more sophisticated informatics capability.
Detecting conversation topics in primary care office visits from transcripts of patient-provider interactions
Authors: Park Jihyun , Kotzias Dimitrios , Kuo Patty , Logan IV Robert L , Merced Kritzia , Singh Sameer , Tanana Michael , Karra Taniskidou Efi , Lafata Jennifer Elston , Atkins David C , Tai-Seale Ming , Imel Zac E , Smyth Padhraic
Published: July 2019

Objective

Amid electronic health records, laboratory tests, and other technology, office-based patient and provider communication is still the heart of primary medical care. Patients typically present multiple complaints, requiring physicians to decide how to balance competing demands. How this time is allocated has implications for patient satisfaction, payments, and quality of care. We investigate the effectiveness of machine learning methods for automated annotation of medical topics in patient-provider dialog transcripts.

Materials and Methods

We used dialog transcripts from 279 primary care visits to predict talk-turn topic labels. Different machine learning models were trained to operate on single or multiple local talk-turns (logistic classifiers, support vector machines, gated recurrent units) as well as sequential models that integrate information across talk-turn sequences (conditional random fields, hidden Markov models, and hierarchical gated recurrent units).

Results

Evaluation was performed using cross-validation to measure 1) classification accuracy for talk-turns and 2) precision, recall, and F1 scores at the visit level. Experimental results showed that sequential models had higher classification accuracy at the talk-turn level and higher precision at the visit level. Independent models had higher recall scores at the visit level compared with sequential models.

Conclusions

Incorporating sequential information across talk-turns improves the accuracy of topic prediction in patient-provider dialog by smoothing out noisy information from talk-turns. Although the results are promising, more advanced prediction techniques and larger labeled datasets will likely be required to achieve prediction performance appropriate for real-world clinical applications.
Identifying relations of medications with adverse drug events using recurrent convolutional neural networks and gradient boosting
Authors: Yang Xi , Bian Jiang , Fang Ruogu , Bjarnadottir Ragnhildur I , Hogan William R , Wu Yonghui
Published: July 2019

Objective

To develop a natural language processing system that identifies relations of medications with adverse drug events from clinical narratives. This project is part of the 2018 n2c2 challenge.

Materials and Methods

We developed a novel clinical named entity recognition method based on an recurrent convolutional neural network and compared it to a recurrent neural network implemented using the long-short term memory architecture, explored methods to integrate medical knowledge as embedding layers in neural networks, and investigated 3 machine learning models, including support vector machines, random forests and gradient boosting for relation classification. The performance of our system was evaluated using annotated data and scripts provided by the 2018 n2c2 organizers.

Results

Our system was among the top ranked. Our best model submitted during this challenge (based on recurrent neural networks and support vector machines) achieved lenient F1 scores of 0.9287 for concept extraction (ranked third), 0.9459 for relation classification (ranked fourth), and 0.8778 for the end-to-end relation extraction (ranked second). We developed a novel named entity recognition model based on a recurrent convolutional neural network and further investigated gradient boosting for relation classification. The new methods improved the lenient F1 scores of the 3 subtasks to 0.9292, 0.9633, and 0.8880, respectively, which are comparable to the best performance reported in this challenge.

Conclusion

This study demonstrated the feasibility of using machine learning methods to extract the relations of medications with adverse drug events from clinical narratives.
Implementation of a Blind Quality Control Program in Blood Alcohol Analysis
Authors: Moral Jackeline , Hundl Callan , Lee Dayong , Neuman Maddisen , Grimaldi Aimee , Cuellar Maria , Stout Peter
Published: July 2019

Declared proficiency tests are limited in their use for testing the performance of the entire system, because analysts are aware that they are being tested. A blind quality control (BQC) is intended to appear as a real case to the analyst to remove any intentional or subconscious bias. A BQC program allows a real-time assessment of the laboratory’s policies and procedures and monitors reliability of casework. In September 2015, the Houston Forensic Science Center (HFSC) began a BQC program in blood alcohol analysis. Between September 2015 and July 2018, HFSC submitted 317 blind cases: 89 negative samples and 228 positive samples at five target concentrations (0.08, 0.15, 0.16, 0.20 and 0.25 g/100 mL; theoretical targets). These blood samples were analyzed by a headspace gas chromatograph interfaced with dual-flame ionization detectors (HS-GC-FID). All negative samples produced `no ethanol detected’ results. The mean (range) of reported blood alcohol concentrations (BACs) for the aforementioned target concentrations was 0.075 (0.073–0.078), 0.144 (0.140–0.148), 0.157 (0.155–0.160), 0.195 (0.192–0.200) and 0.249 (0.242–0.258) g/100 mL, respectively. The average BAC percent differences from the target for the positive blind cases ranged from −0.4 to −6.3%, within our uncertainty of measurement (8.95–9.18%). The rate of alcohol evaporation/degradation was determined negligible. A multiple linear regression analysis was performed to compare the % difference in BAC among five target concentrations, eight analysts, three HS-GC-FID instruments and two pipettes. The variables other than target concentrations showed no significant difference (P > 0.2). While the 0.08 g/100 mL target showed a significantly larger % difference than higher target concentrations (0.15–0.25 g/100 mL), the % differences among the higher targets were not concentration-dependent. Despite difficulties like gaining buy-in from stakeholders and mimicking evidence samples, the implementation of a BQC program has improved processes, shown methods are reliable and added confidence to staff’s testimony in court.
Simplification of a species complex: Two new species of Leucothoidae (Crustacea: Amphipoda) previously attributed to Leucothoe spinicarpa (Abildgaard, 1789) in Florida, U.S.A.
Authors: White Kristine N
Published: July 2019

Leucothoe spinicarpa (Abildgaard, 1789) has long been thought of as a cosmopolitan species; however, relatively recent morphological studies have discovered a species complex previously attributed to L. spinicarpa. Despite this, several species remain hardly distinguishable from the general leucothoid form of L. spinicarpa. Morphological analyses reveal two distinct species in Tampa Bay, Florida, USA, which is supported by molecular mitochondrial COI and nuclear 18S ribosomal DNA data. Leucothoe tunicasp. nov. and L. machidaisp. nov. are described herein. Analyses of DNA sequences from specimens from Tampa Bay, FL, Big Pine Key, FL, and Belize of L. tunicasp. nov. demonstrate intraspecific genetic structure in morphologically identical populations. Therefore, the geographically distant populations of L. tunicasp. nov. thus represent one species with a wide distribution, whereas L. machidaisp. nov. has so far been collected only in Tampa Bay.
Proximity and learning: evidence from a post-WW2 intellectual reparations program
Authors: Bode Rasmus , Buenstorf Guido , Heinisch Dominik P
Published: July 2019

Prior work indicates that proximity facilitates learning, but proximity reflects individual choices. New data on a British post-World War 2 program to detain and interrogate German industrial experts allow us to minimize selection bias and to disentangle individual dimensions of proximity. Our empirical analysis of post-detention patenting activities suggests that cognitive proximity was more important for interactive learning than social and institutional proximity. Detention in the UK increased inventors’ subsequent likelihood of interacting with UK partners as well as their post-detention patent output.
Risk factors for acute exacerbation of idiopathic interstitial pneumonia in patients undergoing lung cancer treatment
Authors: Taya Tetsuya , Chiba Hirofumi , Yamada Gen , Takahashi Mamoru , Ikeda Kimiyuki , Mori Yuki , Otsuka Mitsuo , Takahashi Hiroki
Published: July 2019

Objective

Identifying risk factors for cancer treatment-related acute exacerbations (AEs) of idiopathic interstitial pneumonia (IIP) in patients with lung cancer.

Methods

We retrospectively reviewed clinical records of 98 patients with concurrent lung cancer and IIPs diagnosed and treated at the Sapporo Medical University Hospital from January 2010 to December 2014.

Results

Of the 98 patients with concurrent lung cancer and IIPs, 14 patients (14.3%) had AEs. A total of 10 patients died. The univariate analysis revealed that the patients with idiopathic pulmonary fibrosis (IPF) or usual interstitial pneumonia (UIP) patterns on chest computed tomography (CT) had significantly higher rates of AE than those with non-IPF or non-UIP patterns, respectively. Further, those with a reduced percentage of forced vital capacity (%FVC) predictive values or elevated Krebs von den Lungen-6 (KL-6) presented significantly higher rates of AE. Our multivariate analysis identified that UIP pattern on chest CT and each 10% decrease in %FVC were significant independent risk factors for AEs. Of the 14 patients who experienced AEs, 10 cases were associated with cancer treatment. The treatment-specific incidences were 3/40 (7.5%) for surgery, 5/50 (10.0%) for chemotherapy, and 2/26 (7.7%) for radiation therapy. After comparing the AE incidences in 55 cases receiving one treatment (monotherapy group) and in 29 cases receiving two types of treatment or more (multitherapy group), we found no significant differences.

Conclusions

Chest CT UIP patterns and reduced %FVC are independent risk factors for AE. Moreover, AE incidence did not increase in the multitherapy group compared with the monotherapy group.
Sample preparation utilizing sputter coating increases contrast of cellulose nanocrystals in the transmission electron microscope
Authors: Mulenos Marina R , Zechmann Bernd , Sayes Christie M
Published: July 2019

Cellulose nanocrystals (CNCs) are prepared for transmission electron microscopy (TEM) using positive or negative stains in an effort to increase the contrast between the specimen and background. When imaging CNCs, conventional stains have been shown to induce particle aggregation and produce artifacts. In this study, we report on methods used to image CNCs. To increase contrast and decrease artifacts and aggregation, sputter coating was used to coat the samples. CNCs were loaded onto copper grids and sputter coated with one of four different metals: iridium, carbon, gold, and titanium. The final layer was deposited at 5 nm to ensure surface homogeneity. The thin layer of conductive metal atoms deposited onto the specimen surface significantly increased contrast and improved image quality. The results presented here demonstrate the advantages of using sputter coating for imaging of highly crystalline cellulose materials with TEM.
The Association of Abdominal Adiposity With Mortality in Patients With Stage I–III Colorectal Cancer
Authors: Brown Justin C , Caan Bette J , Prado Carla M , Cespedes Feliciano Elizabeth M , Xiao Jingjie , Kroenke Candyce H , Meyerhardt Jeffrey A
Published: July 2019

Background

The quantity and distribution of adipose tissue may be prognostic measures of mortality in colorectal cancer patients, and such associations may vary by patient sex.

Methods

This cohort included 3262 stage I–III colorectal cancer patients. Visceral and subcutaneous adipose tissues were quantified using computed tomography. The primary endpoint was all-cause mortality. Restricted cubic splines estimated statistical associations with two-sided P values.

Results

Visceral adipose tissue was prognostic of mortality in a reverse L-shaped pattern (nonlinear P = .02); risk was flat to a threshold (∼260 cm2) then increased linearly. Subcutaneous adipose tissue was prognostic of mortality in a J-shaped pattern (nonlinear P < .001); risk was higher at extreme (<50 cm2) but lower at intermediate values (>50 to ≤560 cm2). Patient sex modified the prognostic associations between visceral adipose tissue (Pinteraction = .049) and subcutaneous adipose tissue (Pinteraction = .04) with mortality. Among men, visceral adiposity was associated with mortality in a J-shaped pattern (nonlinear P = .003), whereas among women, visceral adiposity was associated with mortality in a linear pattern (linear P = .008). Among men, subcutaneous adiposity was associated with mortality in an L-shaped pattern (nonlinear P = .01), whereas among women, subcutaneous adiposity was associated with mortality in a J-shaped pattern (nonlinear P < .001).

Conclusions

Visceral and subcutaneous adipose tissue were prognostic of mortality in patients with colorectal cancer; the shape of these associations were often nonlinear and varied by patient sex. These results offer insight into the potential biological mechanisms that link obesity with clinical outcomes in patients with cancer, suggesting that the dysregulated deposition of excess adiposity is prognostic of mortality.
Hyperglycemia During Childhood Cancer Therapy: Incidence, Implications, and Impact on Outcomes
Authors: Grimes Allison , Mohamed Ashraf , Sopfe Jenna , Hill Rachel , Lynch Jane
Published: July 2019

Hyperglycemia is a known complication of therapies used in the treatment of childhood cancer, particularly glucocorticoids and asparaginase. It has been linked to increased infection and reduced survival. With more limited data on hyperglycemia during childhood cancer treatment compared with adult cancer, impact on outcomes is less clear in this population. As additional glycemic-altering cancer agents including immune checkpoint inhibitors and targeted therapies make their way into pediatric cancer treatment, there is a more pressing need to better understand the mechanisms, risk factors, and adverse effects of hyperglycemia on the child with cancer. Thus, we utilized a systematic approach to review the current understanding of the incidence, implications, and outcomes of hyperglycemia during childhood cancer therapy.
High-Fat Diet Intake Promotes the Enlargement and Degenerative Changes in the Media of Intracranial Aneurysms in Rats
Authors: Shimizu Kampei , Miyata Haruka , Abekura Yu , Oka Mieko , Kushamae Mika , Kawamata Takakazu , Mizutani Tohru , Kataoka Hiroharu , Nozaki Kazuhiko , Miyamoto Susumu , Aoki Tomohiro
Published: July 2019

Subarachnoid hemorrhage due to rupture of intracranial aneurysms is a life-threatening disease. Although some previous reports have demonstrated an association between lipid accumulation and degenerative changes in aneurysmal walls in humans, epidemiological studies have failed to identify dyslipidemia as a risk factor for intracranial aneurysms. Thus, we examined whether an increase in serum cholesterol levels facilitates the progression of intracranial aneurysms in a rat model. Rats were given a high-fat diet (HFD) and subjected to an intracranial aneurysm model. The HFD elevated their serum cholesterol levels. The intracranial aneurysms induced at the anterior cerebral artery-olfactory artery bifurcation were significantly larger in the high-fat group than in the normal-chow group. Histological analysis demonstrated that the loss of medial smooth muscle layers was exacerbated in the high-fat group and indicated the presence of macrophage-derived foam cells in the lesions. In in vitro experiments, the expression levels of the pro-inflammatory genes induced by LPS in RAW264.7-derived foam cells were significantly higher than those in RAW264.7 cells. The combination of these results suggests that increased serum cholesterol levels facilitate degenerative changes in the media and the progression of intracranial aneurysms presumably through foam cell transformation.
A case report of retrograde intussusception 3 years post Roux-en-Y gastric bypass
Authors: Okal Fahad , Allarakia Jawad , Alghamdi Amer , Alqurashi Zahid , Aboalsamh Ghaleb , Abdelhady Ahmed
Published: July 2019

Retrograde jejuno-jejunal intussusception is a rare complication of bariatric surgeries. It causes acute sudden symptoms that require immediate surgical intervention. We report a case of a 46-year-old female who underwent Roux-en-Y gastric bypass (REYGP) 3 years prior. The patient presented to the emergency department with acute sudden abdominal pain, nausea and vomiting. Laparoscopically, intussuscepting small bowel segment was found gangrenous, and it was resected and end-to-end anastomoses were fashioned. The postoperative course was uneventful, and the patient remained asymptomatic for the 12 months of follow-up. Patients with retrograde intussusception experience an intolerable severe pain that necessitates surgical intervention. The etiology of intussusception as a complication after REYGP is unclear, yet theoretically some possible etiologies exist. The initial diagnosis of retrograde intussusception is made based on abdominal computed tomography. Early intervention significantly reduces morbidity and mortality.
Laparoscopic removal of rare variant of leiomyoma in the female inguinal canal: a report of two cases
Authors: Byun Geon Young , Koo Bum Hwan , Lee Seung Geun , Kim Myoung Jin , Lee Sung Ryul
Published: July 2019

Angioleiomyoma and lipoleiomyoma are rarely found tumors in the inguinal canal. We present two cases of laparoscopic removal of angioleiomyoma and lipoleiomyoma in the female inguinal canal. In Case 1, a 35-year-old woman was admitted to our hospital with left inguinal swelling and intermittent pain. A hypoechoic well-marginated mass was observed on ultrasonography. Laparoscopic complete tumor excision and posterior wall repair were performed, and a diagnosis of angioleiomyoma was confirmed on histopathological evaluation. In Case 2, a 55-year-old woman was admitted with a painful right inguinal swelling. A hypoechoic well-marginated ovoid mass was observed on ultrasonography. Laparoscopic complete tumor excision and posterior wall repair were performed, and a diagnosis of lipoleiomyoma was confirmed on histopathological evaluation. Laparoscopic tumor excision and posterior wall repair are effective treatments of leiomyomas in the inguinal canal.
Relationship between irradiance and levels of Calvin–Benson cycle and other intermediates in the model eudicot Arabidopsis and the model monocot rice
Authors: Borghi Gian Luca , Moraes Thiago Alexandre , Günther Manuela , Feil Regina , Mengin Virginie , Lunn John E , Stitt Mark , Arrivault Stéphanie
Published: July 2019

Calvin–Benson cycle intermediate profiling in Arabidopsis and rice reveals interspecies differences in pathway operation at moderate irradiance, and shared features that minimize inefficiency in low light and low CO2.
Phosphate acquisition efficiency in wheat is related to root:shoot ratio, strigolactone levels, and PHO2 regulation
Authors: de Souza Campos Pedro M , Cornejo Pablo , Rial Carlos , Borie Fernando , Varela Rosa M , Seguel Alex , López-Ráez Juan Antonio
Published: July 2019

Higher Pi acquisition efficiency in wheat was related to an improved root system under Pi starvation, allowing higher Pi uptake. This response correlated with faster modulation of the IPS1–miR399–PHO2 pathway and strigolactone levels.
Chalutzim—Zionist Photography in Germany and Palestine in the 1930s: A Comparative Analysis of Images
Authors: Pilarczyk Ulrike
Published: July 2019

This article reconstructs and compares photographic perspectives on the historical phenomenon of preparing German-Jewish youth for emigration from Germany, and their subsequent training in Palestinian kibbutzim in the framework of the hachshara and the youth aliyah. It considers the photographers’ status, differentiating between professional photography and the work of amateurs, and investigates the use and addressees of these images. The image analysis that underlies this study examines facets of the photographic and pictorial conception of chalutzian youth, including motifs, style, and atmospheres. In the process, photography is classified as a unique historical image source, in which the conditions of the time inscribe themselves even beyond personal and political intentions, interests, and contexts of usage. The image analysis also aims to reconstruct the specific, visually represented individual and collective experiences of the producers and addressees of photographic images in Germany and Mandatory Palestine.
The elephant in the room: the importance of the details of massive star formation in molecular clouds
Authors: Grudić Michael Y , Hopkins Philip F
Published: July 2019

Most simulations of galaxies and massive giant molecular clouds (GMCs) cannot explicitly resolve the formation (or predict the main-sequence masses) of individual stars. So they must use some prescription for the amount of feedback from an assumed population of massive stars (e.g. sampling the initial mass function, IMF). We perform a methods study of simulations of a star-forming GMC with stellar feedback from UV radiation, varying only the prescription for determining the luminosity of each stellar mass element formed (according to different IMF sampling schemes). We show that different prescriptions can lead to widely varying (factor of ∼3) star formation efficiencies (on GMC scales) even though the average mass-to-light ratios agree. Discreteness of sources is important: radiative feedback from fewer, more-luminous sources has a greater effect for a given total luminosity. These differences can dominate over other, more widely recognized differences between similar literature GMC-scale studies (e.g. numerical methods, cloud initial conditions, presence of magnetic fields). Moreover the differences in these methods are not purely numerical: some make different implicit assumptions about the nature of massive star formation, and this remains deeply uncertain in star formation theory.
Joint estimation of the Epoch of Reionization power spectrum and foregrounds
Authors: Sims Peter H , Pober Jonathan C
Published: July 2019

The power spectrum of redshifted 21 cm emission brightness temperature fluctuations is a powerful probe of the Epoch of Reionization (EoR). However, bright foreground emission presents a significant impediment to its unbiased recovery from interferometric data. We estimate the power spectrum within a Bayesian framework and demonstrate that incorporating a priori knowledge of the spectral structure of foregrounds in the large spectral scale component of the data model enables significantly improved modelling of the foregrounds without increasing the model complexity. We explore two astrophysically motivated parametrizations of the large spectral scale model: (i) a constant plus power-law model of the form $q_{0}+q_{1}(\nu /\nu _{0})^{b_{1}}$ for two values of b1: b1 = 〈β〉GDSE and b1 = 〈β〉EGS, the mean spectral indices of the Galactic diffuse synchrotron emission and extragalactic source foreground emission, respectively; and (ii) a constant plus double power-law model of the form $q_{0}+q_{1}(\nu /\nu _{0})^{b_{1}}+q_{2}(\nu /\nu _{0})^{b_{2}}$ with b1 = 〈β〉GDSE and b2 = 〈β〉EGS. We estimate the EoR power spectrum from simulated interferometric data consisting of an EoR signal, Galactic diffuse synchrotron emission, extragalactic sources, and diffuse free–free emission from the Galaxy. We show that, by jointly estimating a model of the EoR signal with the constant plus double power-law parametrization of the large spectral scale model, unbiased estimates of the EoR power spectrum are recoverable on all spatial scales accessible in the data set, including on the large spatial scales that were found to be contaminated in earlier work.
A stable finite-volume method for scalar field dark matter
Authors: Hopkins Philip F
Published: July 2019

We describe and test a family of new numerical methods to solve the Schrödinger equation in self-gravitating systems, e.g. Bose–Einstein condensates or ‘fuzzy’/ultra-light scalar field dark matter. The methods are finite-volume Godunov schemes with stable, higher order accurate gradient estimation, based on a generalization of recent mesh-free finite-mass Godunov methods. They couple easily to particle-based N-body gravity solvers (with or without other fluids, e.g. baryons), are numerically stable, and computationally efficient. Different sub-methods allow for manifest conservation of mass, momentum, and energy. We consider a variety of test problems and demonstrate that these can accurately recover solutions and remain stable even in noisy, poorly resolved systems, with dramatically reduced noise compared to some other proposed implementations (though certain types of discontinuities remain challenging). This is non-trivial because the ‘quantum pressure’ is neither isotropic nor positive definite and depends on higher order gradients of the density field. We implement and test the method in the code gizmo.
On the ultra-compact nature of the neutron star system 1RXS J170854.4−321857: insights from X-ray spectroscopy
Authors: Armas Padilla M , López-Navas E
Published: July 2019

The relatively small family of ultra-compact X-ray binary systems is of great interest for many areas of astrophysics. We report on a detailed X-ray spectral study of the persistent neutron star low-mass X-ray binary 1RXS J170854.4−321857. We analysed two XMM–Newton observations obtained in late 2004 and early 2005 when, in agreement with previous studies, the system displayed an X-ray luminosity (0.5–10 keV) of ${\sim} 1\times 10^{36}\, \mathrm{erg~s}^{-1}$. The spectrum can be described by a Comptonized emission component with Γ ∼ 1.9 and a distribution of seed photons with a temperature of ∼0.23 keV. A prominent residual feature is present at soft energies, which is reproduced by the absorption model if overabundances of Ne and Fe are allowed. We discuss how similar observables, which might be attributed to the peculiar (non-solar) composition of the plasma donated by the companion star, are a common feature in confirmed and candidate ultra-compact systems. Although this interpretation is still under debate, we conclude that the detection of these features along with the persistent nature of the source at such low luminosity and the intermediate–long burst that it displayed in the past confirms 1RXS J170854.4−321857 as a solid ultra-compact X-ray binary candidate.
Cosmic ray acceleration of cool clouds in the circumgalactic medium
Authors: Wiener Joshua , Zweibel Ellen G , Ruszkowski Mateusz
Published: July 2019

We investigate a mechanism for accelerating cool (104 K) clouds in the circumgalactic medium (CGM) with cosmic rays (CRs), possibly explaining some characteristics of observed high-velocity clouds (HVCs). Enforcing CRs to stream down their pressure gradient into a region of slow streaming speed results in significant build-up of CR pressure which can accelerate the CGM. We present the results of the first two-dimensional magnetohydrodynamic (MHD) simulations of such ‘CR bottlenecks,’ expanding on simpler simulations in 1D. Although much more investigation is required, we find two main results. First, radiative cooling in the interfaces of these clouds is sufficient to keep the cloud intact to CR wave heating. Secondly, cloud acceleration depends almost linearly with the injected CR flux at low values (comparable to that expected from a Milky Way-like star formation rate), but scales sublinearly at higher CR fluxes in 1D simulations. 2D simulations show hints of sublinear dependence at high CR fluxes but are consistent with pure linear dependence up to the CR fluxes tested. It may therefore be plausible to accelerate cool clouds in the CGM to speeds of hundreds of km s−1.
Mean field solar surface dynamo in the presence of partially ionized plasmas and sub-surface shear layer
Authors: Paradkar B S , Chitre S M , Krishan V
Published: July 2019

A non-linear α − Ω dynamo in the partially ionized turbulent plasma in the presence of sub-surface velocity shear is studied with mean-field electrodynamics. Such a dynamo is probably operational in the near-surface region of the Sun, where the presence of both neutrals and the velocity shear (due to sub-surface shear layer in the rotation profile) is observationally well established. In particular, we show that the inclusion of ambipolar diffusion leads to a saturation of magnetic field amplitudes in the α − Ω dynamo. We also demonstrate that the temporal evolution of large-scale global magnetic fields follows the well-known pattern similar to the ‘butterfly’ diagram displayed by sunspots. As usual the velocity shear converts part of the poloidal into the toroidal magnetic field which in turn is regenerated largely by the combined kinetic plus Hall helicity, thus closing the dynamo loop. In addition, by allowing temporal variation in the helicity and ambipolar diffusion coefficient we are able to reproduce the grand-minimum type behaviour of the solar dynamo. Details of theoretical model along with numerical computations of dynamo equations in the partially ionized plasma are outlined. The solar surface dynamo model envisaged in this work could operate in conjunction with the global dynamo present in the bulk of the convection zone.
Angular momentum transport in massive stars and natal neutron star rotation rates
Authors: Ma Linhao , Fuller Jim
Published: July 2019

The internal rotational dynamics of massive stars are poorly understood. If angular momentum (AM) transport between the core and the envelope is inefficient, the large core AM upon core-collapse will produce rapidly rotating neutron stars (NSs). However, observations of low-mass stars suggest an efficient AM transport mechanism is at work, which could drastically reduce NS spin rates. Here, we study the effects of the baroclinic instability and the magnetic Tayler instability in differentially rotating radiative zones. Although the baroclinic instability may occur, the Tayler instability is likely to be more effective for AM transport. We implement Tayler torques as prescribed by Fuller, Piro, and Jermyn into models of massive stars, finding they remove the vast majority of the core’s AM as it contracts between the main-sequence and helium-burning phases of evolution. If core AM is conserved during core-collapse, we predict natal NS rotation periods of $P_{\rm NS} \approx 50\!-\!200 \, {\rm ms}$, suggesting these torques help explain the relatively slow rotation rates of most young NSs, and the rarity of rapidly rotating engine-driven supernovae. Stochastic spin-up via waves just before core-collapse, asymmetric explosions, and various binary evolution scenarios may increase the initial rotation rates of many NSs.
Vertical shear-induced resonant triads in Keplerian discs
Authors: Shtemler Yuri , Mond Michael
Published: July 2019

The vertical-shear instability (VSI) is studied through weakly non-linear analysis of unmagnetized vertically isothermal thin Keplerian discs under small radial temperature gradients. Vertically global and radially local axisymmetric compressible perturbations are considered. The VSI excites three classes of quasi-resonant triads of non-linearly interacting modes characterized by distinct temporal evolution. Most of the triads belong to the two-mode regime of non-linear interaction. Such triads are comprised of one unstable non-linear mode that grows quasi-exponentially, and two other modes that practically decoupled from the former. The latter two modes perform non-linear oscillations around their either linear prototypes (class I) or respective initial values (class II). The rest of the resonant triads belong to class III where all three modes exhibit non-linear oscillations. The proposed model describes an intermediate non-linear stage of the VSI prior to its saturation.
Multiple Plasticity Regulators Reveal Targets Specifying an Induced Predatory Form in Nematodes
Authors: Bui Linh T , Ragsdale Erik J
Published: July 2019

The ability to translate a single genome into multiple phenotypes, or developmental plasticity, defines how phenotype derives from more than just genes. However, to study the evolutionary targets of plasticity and their evolutionary fates, we need to understand how genetic regulators of plasticity control downstream gene expression. Here, we have identified a transcriptional response specific to polyphenism (i.e., discrete plasticity) in the nematode Pristionchus pacificus. This species produces alternative resource-use morphs—microbivorous and predatory forms, differing in the form of their teeth, a morphological novelty—as influenced by resource availability. Transcriptional profiles common to multiple polyphenism-controlling genes in P. pacificus reveal a suite of environmentally sensitive loci, or ultimate target genes, that make up an induced developmental response. Additionally, in vitro assays show that one polyphenism regulator, the nuclear receptor NHR-40, physically binds to promoters with putative HNF4α (the nuclear receptor class including NHR-40) binding sites, suggesting this receptor may directly regulate genes that describe alternative morphs. Among differentially expressed genes were morph-limited genes, highlighting factors with putative “on–off” function in plasticity regulation. Further, predatory morph-biased genes included candidates—namely, all four P. pacificus homologs of Hsp70, which have HNF4α motifs—whose natural variation in expression matches phenotypic differences among P. pacificus wild isolates. In summary, our study links polyphenism regulatory loci to the transcription producing alternative forms of a morphological novelty. Consequently, our findings establish a platform for determining how specific regulators of morph-biased genes may influence selection on plastic phenotypes.
From Root to Tips: Sporulation Evolution and Specialization inBacillus subtilisand the Intestinal PathogenClostridioides difficile
Authors: Ramos-Silva Paula , Serrano Mónica , Henriques Adriano O
Published: July 2019

Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of highly resistant, dormant endospores. Endospores allow environmental persistence, dissemination and for pathogens, are also infection vehicles. In both the model Bacillus subtilis, an aerobic organism, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. Their expression is coordinated between the forespore and the mother cell, the two cells that participate in the process, and is kept in close register with the course of morphogenesis. The evolutionary mechanisms by which sporulation emerged and evolved in these two species, and more broadly across Firmicutes, remain largely unknown. Here, we trace the origin and evolution of sporulation using the genes known to be involved in the process in B. subtilis and C. difficile, and estimating their gain-loss dynamics in a comprehensive bacterial macroevolutionary framework. We show that sporulation evolution was driven by two major gene gain events, the first at the base of the Firmicutes and the second at the base of the B. subtilis group and within the Peptostreptococcaceae family, which includes C. difficile. We also show that early and late sporulation regulons have been coevolving and that sporulation genes entail greater innovation in B. subtilis with many Bacilli lineage-restricted genes. In contrast, C. difficile more often recruits new sporulation genes by horizontal gene transfer, which reflects both its highly mobile genome, the complexity of the gut microbiota, and an adjustment of sporulation to the gut ecosystem.
CircFOXO3 promotes glioblastoma progression by acting as a competing endogenous RNA for NFAT5
Authors: Zhang Shuai , Liao Keman , Miao Zengli , Wang Qing , Miao Yifeng , Guo Zhongye , Qiu Yun , Chen Binghong , Ren Li , Wei Zilong , Lin Yingying , Lu Xiaojie , Qiu Yongming
Published: July 2019

Background

Circular RNAs (circRNAs), a newly discovered type of endogenous noncoding RNA, have been proposed to mediate the progression of diverse types of tumors. Systematic studies of circRNAs have just begun, and the physiological roles of circRNAs remain largely unknown. Here, we focused on elucidating the potential role and molecular mechanism of circular forkhead box O3 (circFOXO3) in glioblastoma (GBM) progression.

Methods

First, we analyzed circFOXO3 alterations in GBM and noncancerous tissues through real-time quantitative reverse transcription PCR (qRT-PCR). Next, we used loss- and gain-of-function approaches to evaluate the effect of circFOXO3 on GBM cell proliferation and invasion. Mechanistically, fluorescent in situ hybridization, RNA pull-down, dual luciferase reporter, and RNA immunoprecipitation assays were performed to confirm the interaction between circFOXO3 and miR-138-5p/miR-432-5p in GBM. An animal model was used to verify the in vitro experimental findings.

Results

CircFOXO3 expression was significantly higher in GBM tissues than in noncancerous tissues. GBM cell proliferation and invasion were reduced by circFOXO3 knockdown and enhanced by circFOXO3 overexpression. Further biochemical analysis showed that circFOXO3 exerted its pro-tumorigenic activity by acting as a competing endogenous RNA (ceRNA) to increase expression of nuclear factor of activated T cells 5 (NFAT5) via sponging both miR-138-5p and miR-432-5p. Notably, tumor inhibition by circFOXO3 downregulation could be reversed by miR-138-5p/miR-432-5p inhibitors in GBM cells. Moreover, GBM cells with lower circFOXO3 expression developed less aggressive tumors in vivo.

Conclusions

Our data demonstrate that circFOXO3 can exert regulatory functions in GBM and that ceRNA-mediated microRNA sequestration might be a potential strategy for GBM therapy.
Recruit fitness and police academy performance: a prospective validation study
Authors: Korre M , Loh K , Eshleman E J , Lessa F S , Porto L G , Christophi C A , Kales S N
Published: July 2019

Background

Police academies need fit recruits to successfully engage in training activities. In a previous retrospective study, we documented that recruits with poor fitness at entry to the academy had significantly lower graduation rates, and we also suggested evidence-based entry-level fitness recommendations.

Aims

To validate our findings in a prospective cohort of police recruits.

Methods

Recruits entering Massachusetts municipal police academies during 2015–16 were followed prospectively until they dropped out, failed or successfully graduated their academy classes. Entry-level fitness was quantified at the start of each training class using: body composition, push-ups, sit-ups, sit-and-reach and 1.5-mile run time. The primary outcome of interest was the odds of failure (not successfully graduating from an academy). We used logistic regression to assess the probability of not graduating, based on entry-level fitness.

Results

On average, successful graduates were leaner and possessed better overall entry-level fitness. After adjusting for age, gender and body mass index, several fitness measures were strongly associated with academy failure: fewer sit-ups completed (OR 9.6 (95% CI 3.5–26.3) (≤15 versus 41–60)); fewer push-ups completed (OR 6.7 (95% CI 2.5–17.5) (≤20 versus 41–60)); and slower run times (OR 18.4 (95% CI 6.8–50.2) (1.5 miles in > 15 min 20 s versus 10 min 37 s to 12 min 33 s)). The prospective study results supported previously suggested minimum entry-level fitness (95% graduation rate) and target (98% graduation rate) recommendations.

Conclusions

Push-ups completed and 1.5-mile run time at police academy entry were successfully validated as predictors of successful academy graduation, while sit-ups were also a strong independent predictor in the prospective study.
Evolution of Lineage-Specific Gene Networks Underlying the Considerable Fruit Shape Diversity in Persimmon
Authors: Maeda Haruka , Akagi Takashi , Onoue Noriyuki , Kono Atsushi , Tao Ryutaro
Published: July 2019

The shapes of plant organs reflect the evolution of each lineage and have been diversified according to lineage-specific adaptations to environment. Research on the molecular pathways responsible for organ shapes has traditionally been focused mainly on leaves or flowers. Thus, little is known about the pathways controlling fruit shapes, despite their diversity in some plant species. In this study, we analyzed oriental persimmon (Diospyros kaki), which exhibits considerable diversity in fruit shapes among cultivars, to elucidate the underlying molecular mechanism using transcriptomic data and quantitative evaluation. First, to filter the candidate genes associated with persimmon fruit shapes, the whole gene expression patterns obtained using mRNA-Seq analysis from 100 individuals, including a segregated population and various cultivars, were assessed to detect correlations with principal component scores for fruit shapes characterized with elliptic Fourier descriptors. Next, a gene co-expression network analysis with weighted gene co-expression network analysis (WGCNA) package revealed that class 1 KNOX family genes and SEEDSTICK function as integrators along with some phytohormone-related genes, to regulate the fruit shape diversity. On the other hand, the OVATE family genes also contribute to fruit shape diversity, of which pathway would be potentially shared with other plant species. Evolutionary aspects suggest that acquisition of a high lineage-specific and variable expression of class 1 KNOX gene, knotted-like homeobox of Arabidopsis thaliana 1 (KNAT1), in young fruit is important for establishing the persimmon-specific mechanism that determines fruit shape diversity.
Quantifying the nativeness of antibody sequences using long short-term memory networks
Authors: Wollacott Andrew M , Xue Chonghua , Qin Qiuyuan , Hua June , Bohnuud Tanggis , Viswanathan Karthik , Kolachalama Vijaya B
Published: July 2019

Antibodies often undergo substantial engineering en route to the generation of a therapeutic candidate with good developability properties. Characterization of antibody libraries has shown that retaining native-like sequence improves the overall quality of the library. Motivated by recent advances in deep learning, we developed a bi-directional long short-term memory (LSTM) network model to make use of the large amount of available antibody sequence information, and use this model to quantify the nativeness of antibody sequences. The model scores sequences for their similarity to naturally occurring antibodies, which can be used as a consideration during design and engineering of libraries. We demonstrate the performance of this approach by training a model on human antibody sequences and show that our method outperforms other approaches at distinguishing human antibodies from those of other species. We show the applicability of this method for the evaluation of synthesized antibody libraries and humanization of mouse antibodies.
Poor Little Rich Kids? The Role of Nature versus Nurture in Wealth and Other Economic Outcomes and Behaviours
Authors: Black Sandra E , Devereux Paul J , Lundborg Petter , Majlesi Kaveh
Published: July 2019

Wealth is highly correlated between parents and their children; however, little is known about the extent to which these relationships are genetic or determined by environmental factors. We use administrative data on the net wealth of a large sample of Swedish adoptees merged with similar information for their biological and adoptive parents. Comparing the relationship between the wealth of adopted and biological parents and that of the adopted child, we find that, even prior to any inheritance, there is a substantial role for environment and a much smaller role for pre-birth factors and we find little evidence that nature/nurture interactions are important. When bequests are taken into account, the role of adoptive parental wealth becomes much stronger. Our findings suggest that wealth transmission is not primarily because children from wealthier families are inherently more talented or more able but that, even in relatively egalitarian Sweden, wealth begets wealth. We further build on the existing literature by providing a more comprehensive view of the role of nature and nurture on intergenerational mobility, looking at a wide range of different outcomes using a common sample and method. We find that environmental influences are relatively more important for wealth-related variables such as savings and investment decisions than for human capital. We conclude by studying consumption as an overall measure of welfare and find that, like wealth, it is more determined by environment than by biology.
The Strategic Effects of Trademark Protection
Authors: Heath Davidson , Mace Christopher
Published: July 2019

We study the effects of trademark protection on firms’ profits and strategy using the 1996 Federal Trademark Dilution Act, which granted additional legal protection to selected trademarks. We find that the FTDA raised treated firms’ operating profits and was followed by a spike in trademark lawsuits and lower entry and exit in affected product markets. Treated firms reduced R&D spending, produced fewer patents and new products, and recalled a higher number of unsafe products. Our results suggest that stronger trademark protection negatively affected innovation and product quality. (JEL D22, K2, L43, O31, O34, O38)

Authors have furnished code/data and an Internet Appendix, which are available on the Oxford University Press Web site next to the link to the final published paper online.