bluuebunny/crossref_metadata_2025 huggingface dataset:
Hyperon weak radiative decay *
Authors: Niu Peng-Yu , Richard Jean-Marc , Wang Qian , Zhao Qiang
Published: October 2020

We revisit the hyperon weak radiative decays in the framework of the non-relativistic constituent quark model. This study confirms the nonlocal feature of the hyperon weak radiative transition operators, which are dominated by the pole terms, and an overall self-consistent description of the available experimental data for the Cabibbo-favored hyperon weak radiative decays is presented. It provides a natural mechanism for evading the Hara theorem, where sizeable parity-violating contributions can come from the intermediate orbital excitations. Cancellations between pole terms also explain the significant SU(3) flavor symmetry breaking manifested by the experimental data. We also discuss several interesting selection rules arising from either the electromagnetic or the weak interaction vertices. These features suggest nontrivial relations among various hyperon decays.
Development of the models of the magnetic shielding system for ITER neutral beam injectors
Authors: Amoskov V M , Bazarov A M , Kukhtin V P , Lamzin E A , Rodin I Y , Sytchevsky S E
Published: October 2020

The paper is devoted to the development of the models of magnetic shielding system for the ITER neutral beam injectors. As the reactor operation is quasistationary, the magnetic field reduction system of the injectors combines a passive magnetic shield and a set of active correction coils. Due to the strict restrictions on the field inside the injectors, precision computations are required during the design stage. A special attention has been paid to possible gaps between steel panels of the passive magnetic shields due to manufacturing and assembly inaccuracies. A set of models with different levels of detail has been built for the convergence study. It was shown that the mesh needs to have tens of millions finite elements to provide the required computational accuracy.
Simulations of parameters of the mirror trap-based neutron source limited by the development of DCLC instability
Authors: Prikhodko V V , Kotelnikov I A , Chernoshtanov I S
Published: October 2020

The axially symmetric mirror trap with deuterium-tritium plasma is considered as a neutron source for the hybrid reactor. The goal of this study is to select the facility parameters, providing the maximum neutron yield at a fixed input power. The procedure is proposed for verifying the sufficient criterion for stability of the drift-cone ion-cyclotron mode. Within a limited set of configurations under consideration, the maximum fusion reaction power of 5.8 MW is achieved at an input power of 100 MW.
Theory of electron motion in combined magnetic trap under conditions of gyromagnetic autoresonance
Authors: Milant’ev V P
Published: October 2020

Using the Bogolyubov method, the solution of equations of electron motion in a combined mirror-type magnetic trap is obtained in cases when the electron approaches the cyclotron resonance region and when it passes through it. It is assumed that the synchronism between particle and the resonator standing wave is maintained by means of slow time variation of the guiding magnetic field. The problem is solved within the framework of the simplified model using the weakly relativistic approximation.
Deuterium ion beam focusing for the point neutron source development
Authors: Golubev S V , Skalyga V A , Izotov I V , Shaposhnikov R A , Razin S V , Bokhanov A F , Kazakov M Yu , Vybin S S , Kiseleva E M , Shlepnev S P
Published: October 2020

This work is a continuation of the studies on the point neutron source development. In the neutron source scheme proposed, neutron emission occurs in a relatively small region (less than 1 mm) as a result of the D–D fusion reaction initiated when the focused deuterium ion beam hits the deuterium-loaded target. The main goal of the project is to develop a simple and compact device that can be used in the high-quality fast neutron radiography. In the scheme proposed, the ion beam is extracted from the dense ECR discharge plasma that is confined in the simple magnetic mirror trap. After upgrading the extraction system and the magnetic lens, the deuterium ion beam with a total current in the focal plane of up to 150 mA was obtained, which considerably exceeds the current obtained previously. The numerical simulations of the beam magnetic focusing were performed using the IBSimu code and the results were compared to the experimental data.
Effect of plasma density gradients on generation of terahertz radiation in magnetized plasma column during relaxation of kiloampere REB inside it
Authors: Arzhannikov A , Annenkov V , Ivanov I , Kalinin P , Kasatov A , Kuznetsov S , Kuklin K , Makarov M , Mekler K , Popov S , Rovenskikh A , Samtsov D , Sandalov E , Sinitsky S , Stepanov V , Timofeev I , Volchok E
Published: October 2020

Generation of terahertz radiation in the magnetized plasma column due to the two-stream instability developing in the relativistic electron beam (REB) with a current of 10 kA is studied at the GOL-PET facility. In the first series of the experiments, at the regular transverse plasma density gradients, power of the generated terahertz radiation increased thirty times. At a frequency of the upper-hybrid oscillations (0.2–0.3 THz) and pulse duration of few microseconds, it reached 4 MWs. In the next experiments, when the additional longitudinal density gradients were created in plasma, the radiation power exceeded 10 MWs. These results are described in this paper.
Measurements of energy absorbed in metal foils during their exposure to plasma jet at the Plasma Focus facility
Authors: Kokololtsev V N , Maslyaev S A , Borovitskaya I V , Nikulin V Ya , Silin P V , Peregudova E N
Published: October 2020

The work presents the results of estimating the energy absorbed in metal foils (copper, aluminium, and vanadium) during their exposure to the high-speed (>107 cm/s) plasma jets generated in a plasma focus facility. The absorbed energy was calculated under assumption that the plasma jet power is not too high, which allowed us to neglect the loss of material due to evaporation. In this case, when the foils were exposed to the single plasma jet, the amount of absorbed energy was determined using data on the mass of the molten metal layer and the ablated melt mass. The energy absorbed in the Al, Cu and V foils calculated in this way turned out to be ~6.5, 5 and 2.1 J, respectively, which is considerably less than the plasma jet energy, which is of the of the order ~100 J.
Spontaneous symmetry breaking and Husimi Q-functions in extended Dicke model
Authors: Seidov S S , Mukhin S I
Published: October 2020

We study the emergence of a parity breaking coherent photonic state of a photon mode coupled to finite array of two-level systems, represented by pseudospins 1/2. The pseudospin-photon interaction is realised via a shift of the photonic oscillator equilibrium position by an amount linear in Cartesian component of the total pseudospin. We demonstrate analytically, that the instability is manifested in an upturn from concave to convex of the ground state energy dependence on the total pseudospin component coupled to the photons. The perturbation, sufficient for parity breaking, tends to zero in the ultrastrong limit of light–matter coupling. We present phase diagram of finite pseudospin-photon system, that demonstrates this feature. Evolution of Husimi Q-functions of the pseudospin and photon subsystems, and of the pseudospin entropy, along different trajectories across the phase diagram is presented.
Electromechanical impedance measurements for bone health monitoring through teeth used as probes of a Piezo-device
Authors: Cardona Carlos I , Tinoco Hector A , Marín-Berrio Maribel L F , García-Grisales Juliana , Gomez Juan P , Roldan-Restrepo Samuel I , Ortiz-Jimenez Juliana
Published: October 2020

Bone is a dynamic biological tissue that acts as the primary rigid support of the body. Several systemic factors are responsible for pathologies that negatively affect its structural attributes. Although the bone is in continuous renewal by osteogenesis, metabolic diseases are the most common affectations that alter its natural equilibrium. Different techniques based on ionizing radiation are used for the bone diagnosis restrictively. However, if these are not used adequately, the application could present risks for human health. In this paper, it is proposed and explored a new technique to apply an early-stage diagnosis of bone variations. The technique evaluates bone structural conditions from the teeth (used as probes) by applying a structural health monitoring (SHM) methodology. An experimental procedure is described to identify the stiffness variations produced by mechanical drillings done in prepared bone samples. The identification is carried out applying the electromechanical impedance technique (EMI) through a piezo-actuated device in the frequency spectrum 5–20kHz. Three bone samples with incorporated teeth (three teeth, two teeth, and one tooth) were prepared to emulate a mandibular portion of alveolar bone-PDL (periodontal ligament)-tooth system. Piezo-device was attached to the crown of the tooth with an orthodontic bracket allowing the teeth to act as probes. The electrical resistance measurements were computed with an electrical decoupling approach that improved the detection of the drillings; it was due to the increment of the sensitivity of the signals. The results showed that the bone mass reduction is correlated with statistical indices obtained in specific frequency intervals of the electrical resistance. This work suggests the possibility of a future application addressed to a bone diagnosis in a non-invasive way.
Quantum computation of eigenvalues within target intervals
Authors: Jensen Phillip W K , Kristensen Lasse Bjørn , Kottmann Jakob S , Aspuru-Guzik Alán
Published: October 2020

There is widespread interest in calculating the energy spectrum of a Hamiltonian, for example to analyze optical spectra and energy deposition by ions in materials. In this study, we propose a quantum algorithm that samples the set of energies within a target energy-interval without requiring good approximations of the target energy-eigenstates. We discuss the implementation of direct and iterative amplification protocols and give resource and runtime estimates. We illustrate initial applications by amplifying excited states on molecular hydrogen.
Prepubertal Internalizing Symptoms and Timing of Puberty Onset in Girls
Authors: Knight Julia A , Kehm Rebecca D , Schwartz Lisa , Frost Caren J , Chung Wendy K , Colonna Sarah , Keegan Theresa H M , Goldberg Mandy , Houghton Lauren C , Hanna Danielle , Glendon Gord , Daly Mary B , Buys Saundra S , Andrulis Irene L , John Esther M , Bradbury Angela R , Terry Mary Beth
Published: October 2020

Stressful environments have been associated with earlier menarche. We hypothesized that anxiety, and possibly other internalizing symptoms, are also associated with earlier puberty in girls. The Lessons in Epidemiology and Genetics of Adult Cancer From Youth (LEGACY) Girls Study (2011–2016) included 1,040 girls aged 6–13 years at recruitment whose growth and development were assessed every 6 months. Prepubertal maternal reports of daughter’s internalizing symptoms were available for breast onset (n = 447), pubic hair onset (n = 456), and menarche (n = 681). Using Cox proportional hazard regression, we estimated prospective hazard ratios and 95% confidence intervals for the relationship between 1 standard deviation of the percentiles of prepubertal anxiety, depression, and somatization symptoms and the timing of each pubertal outcome. Multivariable models included age, race/ethnicity, study center, maternal education, body mass index percentile, and family history of breast cancer. Additional models included maternal self-reported anxiety. A 1–standard deviation increase in maternally reported anxiety in girls at baseline was associated with earlier subsequent onset of breast (hazard ratio (HR) = 1.22, 95% confidence interval (CI): 1.09, 1.36) and pubic hair (HR = 1.15, 95% CI: 1.01, 1.30) development, but not menarche (HR = 0.94, 95% CI: 0.83, 1.07). The association of anxiety with earlier breast development persisted after adjustment for maternal anxiety. Increased anxiety in young girls may indicate risk for earlier pubertal onset.
FEATS: feature selection-based clustering of single-cell RNA-seq data
Authors: Vans Edwin , Patil Ashwini , Sharma Alok
Published: October 2020

Motivation

Advances in next-generation sequencing have made it possible to carry out transcriptomic studies at single-cell resolution and generate vast amounts of single-cell RNA sequencing (RNA-seq) data rapidly. Thus, tools to analyze this data need to evolve as well as to improve accuracy and efficiency.

Results

We present FEATS, a Python software package, that performs clustering on single-cell RNA-seq data. FEATS is capable of performing multiple tasks such as estimating the number of clusters, conducting outlier detection and integrating data from various experiments. We develop a univariate feature selection-based approach for clustering, which involves the selection of top informative features to improve clustering performance. This is motivated by the fact that cell types are often manually determined using the expression of only a few known marker genes. On a variety of single-cell RNA-seq datasets, FEATS gives superior performance compared with the current tools, in terms of adjusted Rand index and estimating the number of clusters. It achieves a 22% improvement in clustering and more accurately estimates the number of clusters when compared with other tools. In addition to cluster estimation, FEATS also performs outlier detection and data integration while giving an excellent computational performance. Thus, FEATS is a comprehensive clustering tool capable of addressing the challenges during the clustering of single-cell RNA-seq data.

Availability

The installation instructions and documentation of FEATS is available at https://edwinv87.github.io/feats/.

Supplementary Data

Supplementary data are available online at https://academic.oup.com/bib.
Systematic characterization and prediction of coenzyme A-associated proteins using sequence and network information
Authors: Fan Bing-Liang , Jiang Zheng , Sun Jun , Liu Rong
Published: October 2020

Coenzyme A-associated proteins (CAPs) are a category of functionally important proteins involved in multiple biological processes through interactions with coenzyme A (CoA). To date, unfortunately, the specific differences between CAPs and other proteins have yet to be systemically investigated. Moreover, there are no computational methods that can be used specifically to predict these proteins. Herein, we characterized CAPs from multifaceted viewpoints and revealed their specific preferences. Compared with other proteins, CAPs were more likely to possess binding regions for CoA and its derivatives, were evolutionarily highly conserved, exhibited ordered and hydrophobic structural conformations, and tended to be densely located in protein–protein interaction networks. Based on these biological insights, we built seven classifiers using predicted CoA-binding residue distributions, word embedding vectors, remote homolog numbers, evolutionary conservation, amino acid composition, predicted structural features and network properties. These classifiers could effectively identify CAPs in Homo sapiens, Mus musculus and Arabidopsis thaliana. The complementarity among the individual classifiers prompted us to build a two-layer stacking model named CAPE for improving prediction performance. We applied CAPE to identify some high-confidence candidates in the three species, which were tightly associated with the known functions of CAPs. Finally, we extended our algorithm to cross-species prediction, thereby developing a generic CAP prediction model. In summary, this work provides a comprehensive survey and an effective predictor for CAPs, which can help uncover the interplay between CoA and functionally relevant proteins.
Deep learning for brain disorders: from data processing to disease treatment
Authors: Burgos Ninon , Bottani Simona , Faouzi Johann , Thibeau-Sutre Elina , Colliot Olivier
Published: October 2020

In order to reach precision medicine and improve patients’ quality of life, machine learning is increasingly used in medicine. Brain disorders are often complex and heterogeneous, and several modalities such as demographic, clinical, imaging, genetics and environmental data have been studied to improve their understanding. Deep learning, a subpart of machine learning, provides complex algorithms that can learn from such various data. It has become state of the art in numerous fields, including computer vision and natural language processing, and is also growingly applied in medicine. In this article, we review the use of deep learning for brain disorders. More specifically, we identify the main applications, the concerned disorders and the types of architectures and data used. Finally, we provide guidelines to bridge the gap between research studies and clinical routine.
Linking the Rapid Cascade of Visuo-Attentional Processes to Successful Memory Encoding
Authors: Geib B R , Cabeza R , Woldorff M G
Published: October 2020

While it is broadly accepted that attention modulates memory, the contribution of specific rapid attentional processes to successful encoding is largely unknown. To investigate this issue, we leveraged the high temporal resolution of electroencephalographic recordings to directly link a cascade of visuo-attentional neural processes to successful encoding: namely (1) the N2pc (peaking ~200 ms), which reflects stimulus-specific attentional orienting and allocation, (2) the sustained posterior-contralateral negativity (post-N2pc), which has been associated with sustained visual processing, (3) the contralateral reduction in oscillatory alpha power (contralateral reduction in alpha > 200 ms), which has also been independently related to attentionally sustained visual processing. Each of these visuo-attentional processes was robustly predictive of successful encoding, and, moreover, each enhanced memory independently of the classic, longer-latency, conceptually related, difference-due-to memory (Dm) effect. Early latency midfrontal theta power also promoted successful encoding, with at least part of this influence being mediated by the later latency Dm effect. These findings markedly expand current knowledge by helping to elucidate the intimate relationship between attentional modulations of perceptual processing and effective encoding for later memory retrieval.
Comparative Effectiveness of Switching to Daptomycin Versus Remaining on Vancomycin Among Patients With Methicillin-resistant Staphylococcus aureus (MRSA) Bloodstream Infections
Authors: Schweizer Marin L , Richardson Kelly , Vaughan Sarrazin Mary S , Goto Michihiko , Livorsi Daniel J , Nair Rajeshwari , Alexander Bruce , Beck Brice F , Jones Michael P , Puig-Asensio Mireia , Suh Daniel , Ohl Madeline , Perencevich Eli N
Published: October 2020

Background

Patients with methicillin-resistant Staphylococcus aureus bloodstream infections (MRSA BSI) usually receive initial treatment with vancomycin but may be switched to daptomycin for definitive therapy, especially if treatment failure is suspected. Our objective was to evaluate the effectiveness of switching from vancomycin to daptomycin compared with remaining on vancomycin among patients with MRSA BSI.

Methods

Patients admitted to 124 Veterans Affairs Hospitals who experienced MRSA BSI and were treated with vancomycin during 2007–2014 were included. The association between switching to daptomycin and 30-day mortality was assessed using Cox regression models. Separate models were created for switching to daptomycin any time during the first hospitalization and for switching within 3 days of receiving vancomycin.

Results

In total, 7411 patients received vancomycin for MRSA BSI. Also, 606 (8.2%) patients switched from vancomycin to daptomycin during the first hospitalization, and 108 (1.5%) switched from vancomycin to daptomycin within 3 days of starting vancomycin. In the multivariable analysis, switching to daptomycin within 3 days was significantly associated with lower 30-day mortality (hazards ratio [HR] = 0.48; 95% confidence interval [CI]: .25, .92). However, switching to daptomycin at any time during the first hospitalization was not significantly associated with 30-day mortality (HR: 0.87; 95% CI: .69, 1.09).

Conclusions

Switching to daptomycin within 3 days of initial receipt of vancomycin is associated with lower 30-day mortality among patients with MRSA BSI. This benefit was not seen when the switch occurred later. Future studies should prospectively assess the benefit of early switching from vancomycin to other anti-MRSA antibiotics.
Did the introduction and increased prescribing of antidepressants lead to changes in long-term trends of suicide rates?
Authors: Amendola Simone , Plöderl Martin , Hengartner Michael P
Published: October 2020

Background

Ecological studies have explored associations between suicide rates and antidepressant prescriptions in the population, but most of them are limited as they analyzed short-term correlations that may be spurious. The aim of this long-term study was to examine whether trends in suicide rates changed in three European countries when the first antidepressants were introduced in 1960 and when prescription rates increased steeply after 1990 with the introduction of the serotonin reuptake inhibitors (SSRIs).

Methods

Data were extracted from the WHO Mortality Database. Suicide rates were calculated for people aged 10–89 years from 1951–2015 for Italy, 1955–2016 for Austria and 1951–2013 for Switzerland. Trends in suicide rates stratified by gender were analyzed using joinpoint regression models.

Results

There was a general pattern of long-term trends that was broadly consistent across all three countries. Suicide rates were stable or decreasing during the 1950s and 1960s, they rose during the 1970s, peaked in the early 1980s and thereafter they declined. There were a few notable exceptions to these general trends. In Italian men, suicide rates increased until 1997, then fell sharply until 2006 and increased again from 2006 to 2015. In women from all three countries, there was an extended period during the 2000s when suicide rates were stable. No trend changes occurred around 1960 or 1990.

Conclusions

The introduction of antidepressants around 1960 and the sharp increase in prescriptions after 1990 with the introduction of the SSRIs did not coincide with trend changes in suicide rates in Italy, Austria or Switzerland.
Philippe Hurault de Cheverny (1528–99) and the Making of Memoirs in Early Modern France
Authors: Virastau Nicolae
Published: October 2020

Memoirs occupy a privileged position in the history of French literature. Historians of French memoirs consider the
Memoires d’Estat
of Chancellor Philippe Hurault de Cheverny to be a stepping stone in the history of self-writing because they seem to mark a transition from self-narratives focusing on the author’s public persona to a self-writing that emphasizes the author’s private life, that is, to something more akin to modern autobiography. Unlike most autobiographical works printed at the time, Cheverny’s memoirs integrate details about the author’s private life and family affairs into the more common first-person chronicle of his public career. A closer examination reveals, however, that multiple practices of self-writing are at work in Cheverny’s book, and that its apparent originality in the history of memoirs and their relation to autobiography more generally are an effect of editorial changes made after the author’s death. The article argues that practices of collective writing and editing of personal documents were common in the early modern age.
Retrospective Analysis of Pediatric and Adult Populations Using an LC-MS/MS Method for Oxcarbazepine/Eslicarbazepine Metabolite
Authors: Kroner Grace M , Thomas Ronald L , Johnson-Davis Kamisha L
Published: October 2020

Background

Therapeutic drug monitoring of anti-epileptic drugs is important to manage seizure control in patients with epilepsy. Oxcarbazepine is a second-generation anti-epileptic drug approved for use in pediatric patients, and eslicarbazepine acetate is a newer generation drug used as adjunctive therapy and monotherapy for partial-onset (focal) seizures. While several second and third generation anti-epileptic drugs have broader therapeutic efficacy in patients, these drugs can still have severe side effects and variable interpatient pharmacokinetics. Consequently, there is a need for accurate and sensitive analytical methods to support therapeutic drug monitoring.

Methods

An assay improvement for a LC-MS/MS method was developed for the major metabolite of oxcarbazepine and eslicarbazepine, licarbazepine (MHD), using a 13C-labeled form of the compound as the internal standard. Additionally, retrospective data analysis was used to compare the distribution of results observed in adult vs pediatric patients.

Results

Accuracy and linearity across the analytical measuring range of 1 to 60 µg/mL was acceptable. Inter- and intra-run precision was less than 6% at 3 concentrations tested. The limit of detection was determined to be 0.5 µg/mL. Significant interference from hemolysis, icterus, lipemia, or 187 other potential interferences was not detected.

Conclusions

The improved assay for MHD was appropriate for clinical use. Retrospective data analysis showed that pediatric and adult patients had a similar distribution of oxcarbazepine/eslicarbazepine metabolite concentrations in serum.
Quality Assessment and Antioxidant Activities of the Blossoms ofInula NervosaWall
Authors: Hu Li-Xia , Luo Mei-Feng , Guo Wen-Jing , He Xiao , Zhou Jun , Qiu Xiao-Yu , Gong Jian-Ping , Li Meng-Chu , Chen Xin-Tao , Wu Dong , Huang Wen-Ping
Published: October 2020

Background

Currently, although Inula nervosa Wall is substantially investigated, little is understood about blossoms of Inula nervosa Wall (BINW).

Objective

In this work, we systematically investigated the antioxidant activity of the extract from BINW by various standard assays including 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical ability, 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) di-ammonium salt radical cation (ABTS), and ferric reducing antioxidant potential (FRAP).

Methods

Chemical compounds were tentatively identified through an UHPLC-QTOF-MS system. Furthermore, the contents of nine compounds were detected with UHPLC method coupled with photodiode array (PDA) detector. By carefully analyzing the quantitative data via clusters analysis and principal component analysis (PCA).

Results

Forty-six compounds were tentatively identified, and our results showed that nine compound samples in 21 batches of BINW collected from different areas could be differentiated and analyzed by a heatmap visualization. In addition, the contents of nine compounds (flavonoids, phenolic acids) exhibited a total of higher amounts and better antioxidant activities from Yunnan than those from the other three origins.

Conclusions

Our study not only developed a powerful platform to explain the difference between traditional Chinese medicines species that are closely related through the chemometric and chemical profiling, but also presented a useful method to establish quality criteria of BINW with multiple origins.

Highlights

To characterize the BINW in detail, we not only performed DPPH, FRAP, and ABTS assays to investigate its antioxidant activity, but also established UHPLC-QTOF-MS/MS- and UHPLC-PDA-based methods to comprehensively identify and qualitatively analyze its components.
An index framework founded on the future profit potential of female beef cattle to aid the identification of candidates for culling
Authors: Dunne Fíona L , Berry Donagh P , Kelleher Margaret M , Evans Ross D , Walsh Siobhan W , Amer Peter R
Published: October 2020

Meticulous culling decisions, coupled with careful breeding decisions, are fundamental to shifting a population distribution in the favorable direction and improving profit per cow. Nevertheless, there is a paucity of easy-to-use dynamic tools to aid in culling decisions in beef cattle. The motivation for the present study was to develop a monetary-based culling tool, here referred to as the Beef Female’s Profit Potential (BFPP), to identify females for culling. The BFPP reflects the expected lifetime profitability of an individual female in a herd for the expected remainder of her lifetime; this profit included that of the beef female herself as well as her progeny. The BFPP index framework was composed of 4 subindexes reflecting the value of an animal: (1) as a nulliparae (this was voided if the cow had already calved), (2) for the remainder of her current parity, (3) summed across each of her expected remaining parities, and (4) when she is retained within the herd and not voluntarily culled. Each subindex was comprised of different components reflecting both genetic and non-genetic effects associated with each female. Transition matrices predicting the expected longevity of each female and their expected month of calving were also utilized in calculating the expected remaining lifetime profitability of each female. The BFPP index was validated on 21,102 beef cows as well as their harvested progeny from 875 herds by stratifying the cows, within herd, into 4 strata based on their BFPP. The mean of the within-herd correlation between the BFPP and the Irish national replacement (i.e., breeding) index was, on average, 0.45 indicating the shortcomings of the breeding index as a culling tool. Cows within the top BFPP stratum had a genetic expectation of accruing almost an additional €36 profit per calving, relative to cows within the worst stratum; when validated on the cow’s own calving interval and survival performance as well as their progeny’s carcass performance, the actual phenotypic value was estimated to be an additional €32 profit per calving. A proportion of this additional profit was due to the harvested progeny of the high BFPP cows having, on average, heavier, more conformed carcasses with less fat cover relative to their poor BFPP contemporaries. This BFPP framework is a useful and easy-to-use tool to aid in producer decision making on the choice of females to voluntarily cull but also on which replacement heifers to graduate into the mature herd.
“The Noblest Roman of them all?” Professional versus Popular Views of America’s Country Doctors
Authors: Borst Charlotte G
Published: October 2020

This essay studies the images, perceptions, and values of the professional medical journals, as well as popular sources such as magazine and films, to show that the country doctor was a contested figure in the late nineteenth and early twentieth centuries. The country doctor’s image embodied competing ideals of a racialized professional and masculine identity that included both place as well as visions of science. Medical professionals pressed an image in their journals and professional advice books that mapped a celebration of science and its predictive value onto urban places that were enshrined in hospitals and laboratory facilities. The public, while embracing this image, also embraced a second one shown in popular media that glorified the self-sacrificing rural solo practitioner. This practitioner’s wisdom came from long contact with patients, he was dedicated to seeing patients in their homes, and his identity was based in the larger needs of the entire community.
Multilevel and Tail Risk Management
Authors: Khalaf Lynda , Leccadito Arturo , Urga Giovanni
Published: October 2020

We introduce backtesting methods to assess Value-at-Risk (VaR) and expected shortfall (ES) that require no more than desktop VaR violations as inputs. Maintaining an integrated VaR perspective, our methodology relies on multiple testing to combine evidence on the frequency and dynamic evolution of violations, and to capture more information than a single threshold can provide about the magnitude of violations. Contributions include a formal finite sample analysis of the joint distribution of multi-threshold violations, and limiting results that unify discrete and continuous definitions of cumulative violations across thresholds. Simulation studies demonstrate the power advantages of the proposed tests, particularly with small samples and when underlying models are unavailable to assessors. Results also reinforce the usefulness of CaViaR approaches not just for VaR but also as ES back-tests. Empirically, we assess desktop data by Bloomberg on exchange traded funds. We find that tail risk is not adequately reflected via a wide spectrum of models and available measures. Results provide useful prescriptions for empirical practice and, more generally, reinforce the recent arguments in favor of combined tests and forecasts in tail risk management.
Metastatic melanoma of the spleen without known primary
Authors: Dusseau Brian , Onders Bridget , Radulescu Andrei , Abourezk Matthew , Leff John
Published: October 2020

We present the case of a patient who underwent a laparoscopic splenectomy for splenomegaly associated with anemia and thrombocytopenia thought to be secondary to lymphoma and was found to have metastatic melanoma without a primary source. This is a rare entity in that the patient falls into an atypical population group with conflicting opinions about management that has been scarcely reported in the literature.
Mutual inclinations between giant planets and their debris discs in HD 113337 and HD 38529
Authors: Xuan Jerry W , Kennedy Grant M , Wyatt Mark C , Yelverton Ben
Published: October 2020

HD 113337 and HD 38529 host pairs of giant planets, a debris disc, and wide M-type stellar companions. We measure the disc orientation with resolved images from Herschel and constrain the three-dimensional orbits of the outer planets with Gaia DR2 and Hipparcos astrometry. Resolved disc modelling leaves degeneracy in the disc orientation, so we derive four separate planet–disc mutual inclination (ΔI) solutions. The most aligned solutions give ΔI = 17°–32° for HD 113337 and ΔI = 21°–45○ for HD 38529 (both 1σ). In both systems, there is a small probability (<0.3 per cent) that the planet and disc are nearly aligned (ΔI < 3○). The stellar and planetary companions cause the orbits of disc material to precess about a plane defined by the forced inclination. We determine this as well as the precession time-scale to interpret the mutual inclination results. We find that the debris discs in both systems could be warped via joint influences of the outer planet and stellar companion, potentially explaining the observed misalignments. However, this requires HD 113337 to be old (0.8–1.7 Gyr), whereas if young (14–21 Myr), the observed misalignment in HD 113337 could be inherited from the protoplanetary disc phase. For both systems, the inclination of the stellar spin axis is consistent with the disc and outer planet inclinations, which instead supports system-wide alignment or near alignment. High-resolution observations of the discs and improved constraints on the planetary orbits would provide firmer conclusions about the (mis)alignment status.
The changing circumgalactic medium over the last 10 Gyr – I. Physical and dynamical properties
Authors: Huscher Ezra , Oppenheimer Benjamin D , Lonardi Alice , Crain Robert A , Richings Alexander J , Schaye Joop
Published: October 2020

We present an analysis of the physical and dynamical states of two sets of EAGLE zoom simulations of galaxy haloes, one at high redshift (z = 2−3) and the other at low redshift (z = 0), with masses of ≈1012 M⊙. Our focus is how the circumgalactic medium (CGM) of these L* star-forming galaxies change over the last 10 Gyr. We find that the high-z CGM is almost equally divided between the ‘cool’ (T < 105 K) and ‘hot’ (T ≥ 105 K) phases, while at low-z the hot CGM phase contains 5 × more mass than the cool phase. The high-z hot CGM contains 60 per cent more metals than the cool CGM, while the low-z cool CGM contains 35 per cent more metals than the hot CGM. The metals are evenly distributed radially between the hot and cool phases throughout the high-z CGM. At high z, the CGM volume is dominated by hot outflows, but also contains cool gas mainly inflowing and cool metals mainly outflowing. At low z, the cool metals dominate the interior and the hot metals are more prevalent at larger radii. The low-z cool CGM has tangential motions consistent with rotational support out to 0.2R200, often exhibiting r ≈ 40 kpc disc-like structures. The low-z hot CGM has several times greater angular momentum than the cool CGM, and a more flattened radial density profile than the high-z hot CGM. This study verifies that, just as galaxies demonstrate significant transformations over cosmic time, the gaseous haloes surrounding them also undergo considerable changes of their own both in physical characteristics of density, temperature, and metallicity, and dynamic properties of velocity and angular momentum.
Ridges in the Dark Energy Survey for cosmic trough identification
Authors: Moews Ben , Schmitz Morgan A , Lawler Andrew J , Zuntz Joe , Malz Alex I , de Souza Rafael S , Vilalta Ricardo , Krone-Martins Alberto , Ishida Emille E O ,   for the COIN Collaboration
Published: October 2020

Cosmic voids and their corresponding redshift-projected mass densities, known as troughs, play an important role in our attempt to model the large-scale structure of the Universe. Understanding these structures enables us to compare the standard model with alternative cosmologies, constrain the dark energy equation of state, and distinguish between different gravitational theories. In this paper, we extend the subspace-constrained mean shift algorithm, a recently introduced method to estimate density ridges, and apply it to 2D weak lensing mass density maps from the Dark Energy Survey Y1 data release to identify curvilinear filamentary structures. We compare the obtained ridges with previous approaches to extract trough structure in the same data, and apply curvelets as an alternative wavelet-based method to constrain densities. We then invoke the Wasserstein distance between noisy and noiseless simulations to validate the denoising capabilities of our method. Our results demonstrate the viability of ridge estimation as a precursor for denoising weak lensing observables to recover the large-scale structure, paving the way for a more versatile and effective search for troughs.
Altered rRNA processing disrupts nuclear RNA homeostasis via competition for the poly(A)-binding protein Nab2
Authors: Aguilar Lisbeth-Carolina , Paul Biplab , Reiter Taylor , Gendron Louis , Arul Nambi Rajan Arvind , Montpetit Rachel , Trahan Christian , Pechmann Sebastian , Oeffinger Marlene , Montpetit Ben
Published: October 2020

RNA-binding proteins (RBPs) are key mediators of RNA metabolism. Whereas some RBPs exhibit narrow transcript specificity, others function broadly across both coding and non-coding RNAs. Here, in Saccharomyces cerevisiae, we demonstrate that changes in RBP availability caused by disruptions to distinct cellular processes promote a common global breakdown in RNA metabolism and nuclear RNA homeostasis. Our data shows that stabilization of aberrant ribosomal RNA (rRNA) precursors in an enp1-1 mutant causes phenotypes similar to RNA exosome mutants due to nucleolar sequestration of the poly(A)-binding protein (PABP) Nab2. Decreased nuclear PABP availability is accompanied by genome-wide changes in RNA metabolism, including increased pervasive transcripts levels and snoRNA processing defects. These phenotypes are mitigated by overexpression of PABPs, inhibition of rDNA transcription, or alterations in TRAMP activity. Our results highlight the need for cells to maintain poly(A)-RNA levels in balance with PABPs and other RBPs with mutable substrate specificity across nucleoplasmic and nucleolar RNA processes.
Maternal-infant nutrition and development programming of offspring appetite and obesity
Authors: Desai Mina , Ross Michael G
Published: October 2020

In the United States and Mexico, the obesity epidemic represents a significant public health problem. Although obesity is often attributed to a Western-style, high-fat diet and decreased activity, there is now compelling evidence that this, in part, occurs because of the developmental programming effects resulting from exposure to maternal overnutrition. Human and animal studies demonstrate that maternal obesity and high-fat diet result in an increased risk for childhood and adult obesity. The potential programming effects of obesity have been partly attributed to hyperphagia, which occurs as a result of increased appetite with reduced satiety neuropeptides or neurons. However, depending on maternal nutritional status during the nursing period, the programmed hyperphagia and obesity can be exacerbated or prevented in offspring born to obese mothers. The underlying mechanism of this phenomenon likely involves the plasticity of the appetite regulatory center and thus presents an opportunity to modulate feeding and satiety regulation and break the obesity cycle.
METHODOLOGY FOR SIMPLE SPOT MEASUREMENT OF EQUILIBRIUM EQUIVALENT RADON CONCENTRATION
Authors: Sakoda Akihiro , Ishimori Yuu , Kanzaki Norie , Tanaka Hiroshi
Published: October 2020

Estimation of the effective inhalation dose of short half-life radon progeny requires the quantification of radon equilibrium equivalent activity concentrations (EEC, Ceq). The aim of the present study is to develop new methodology that focuses on spot measurements to determine EEC from single gross alpha counts and determine an optimised protocol. The core of the approach is to measure alpha particles over time when the radon progeny attached to the sampling filter are significantly disintegrated. The calibration curve of single counts to EEC is theoretically deduced and validated by a comparison test. The advantage of the present method is its minimal requirements, including the use of common instruments and simple sampling, alpha counting and analysis procedures. This approach offers an option for radon practitioners working in a variety of fields, as well as the possibility for non-experts to easily measure Ceq.
Pelleting and starch characteristics of diets containing different corn varieties
Authors: Truelock Courtney N , Tokach Mike D , Stark Charles R , Paulk Chad B
Published: October 2020

This experiment determined the effects of die thickness and conditioning temperature on pelleting and starch characteristics in diets containing conventional or Enogen Feed corn (Syngenta Seeds, LLC). Treatments were arranged as a 2 × 2 × 3 factorial of corn type [conventional (CON) and Enogen Feed corn [EFC]), die thickness [5.6 and 8 length:diameter (L:D)], and conditioning temperature (74, 79, and 85 °C). Diets were steam conditioned (Wenger twin staff preconditioner, Model 150) and pelleted (CPM, Model 1012-2) with a 4- × 22.2-mm (L:D 5.6) or 4- × 31.8-mm (L:D 8) pellet die. Conditioner retention time was set at 30 s and production rate was set at 15 kg/min. All treatments were represented within three replicate days. Pellets were composited and analyzed for gelatinized starch and pellet durability index (PDI). Conditioning temperature, hot pellet temperature, production rate, and pellet mill energy consumption were recorded throughout each processing run. Data were analyzed using the GLIMMIX procedure in SAS (v. 9.4, SAS Institute Inc., Cary, NC) with pelleting run as the experimental unit and day as the blocking factor. Pelleting with a larger die L:D improved PDI (P = 0.01) and increased (P = 0.02) pellet mill energy consumption. Increasing conditioning temperature from 74 to 85 °C increased (linear, P < 0.03) PDI and tended to decrease energy consumption (quadratic, P = 0.07). There was a corn × conditioning temperature interaction (P = 0.01) for gelatinized starch in conditioned mash. Enogen Feed corn diets steam conditioned at 85 °C had the greatest quantity of gelatinized starch. Cooked starch in conditioned mash and pellets was greater (P < 0.01) for EFC diets compared to CON diets and increased (linear, P < 0.01) with increasing conditioning temperature in conditioned mash. Similarly, starch gelatinization was greater (P < 0.01) in pelleted EFC diets compared to CON diets and was increased (linear, P = 0.05) by increasing conditioning temperature from 74 to 85 °C. In conclusion, increasing die L:D and increasing conditioning temperature improved PDI. Starch gelatinization was increased when diets were pelleted at the highest conditioning temperature of 85 °C, and EFC diets resulted in greater starch gelatinization than conventional corn.
Effect of elevated gibberellic acid application on growth and gene expression patterns in white spruce families from a tree improvement program in Alberta, Canada
Authors: Galeano Esteban , Thomas Barb R
Published: October 2020

Nine open-pollinated families of Picea glauca (Moench) Voss from the Region D1 Controlled Parentage Program (Alberta, Canada) were systematically chosen from fast, medium and slow-growth rankings based on breeding values for height from field progeny tests at age 30 years. Seeds from these families were sown and grown to age 3 years to analyze the performance and correlations of growth, physiological traits and expression of gibberellin-related genes, with and without elevated gibberellic acid 3 (GA3) application, under greenhouse conditions. We observed a significant interaction effect between families and growth groups subjected to 50 μg μl−1 of GA3 treatment, causing a decrease in apical internode length, diameter, volume and absolute transcript level for fast-growing families but an increase for families in the slow-growth group for the same traits. We also observed that in the apical internode, the gene PgGA20ox1 had significantly more relative expression under the elevated GA3 treatment than the control trees. In the stem, PgGA3ox1 showed a significantly higher relative expression under elevated GA3 treatment compared with control trees. Also, the slow-growth group showed more relative expression of PgGA20ox1 (in the apical internode) and PgGA3ox1 (in the stem) than the fast-growth group. The apical internode length and diameter significantly increased by 24% and 16%, respectively, with the hormone treatment in the slow growing group. In general, the PgGID1 and PgDELLA1 genes were upregulated and downregulated respectively, in spruce shoots under the GA3 treatment, meaning a positive feedback regulation by those genes were influencing PgGA20ox1 and PgGA3ox1 expression in that tissue type. Moreover, there was a significant correlation between absolute transcript levels of PgGA20ox1 in the apical internode and apical internode length, and absolute transcript levels of PgGA3ox1 in the stem and the diameter, in the fast-growth group families. This study shows that expression of GA genes is a limiting factor for growth in certain white spruce families with a complex feedback mechanism. Finally, absolute transcript levels of endogenous GA relative to growth parameters in juvenile seedlings could potentially be used to accelerate the early selection of families with inherently rapid apical and radial growth expansion.