bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence of penalties method to study excited states using VQE
Authors: Carobene R , Barison S , Giachero A 
Published: May 2023

Abstract
We propose an extension of the variational quantum eigensolver (VQE) that leads to more accurate energy estimations and can be used to study excited states. The method is based on the introduction of a sequence of increasing penalties in the cost function. This approach does not require circuit modifications and thus can be applied with no additional depth cost. Through numerical simulations, we show that we are able to produce variational states with desired physical properties, such as total spin and charge. We assess its performance both on classical simulators and on currently available quantum devices, calculating the potential energy curves of small molecular systems in different physical configurations. Finally, we compare our method to the original VQE and to another extension, obtaining a better agreement with exact simulations for both energy and targeted physical quantities.
Land use effects of biofuel production in the US
Authors: Wang Weiwei , Khanna Madhu 
Published: May 2023

Abstract
Biodiesel production from soybean has been growing in the United States and although its amount is small by comparison with corn ethanol, its addition to existing demands on land can have nonlinear effects on land use, due to an upward sloping and increasingly inelastic supply of land. It is critical to quantify these effects to inform future policies that may expand production of soy biodiesel. Here we apply a multi-period, partial equilibrium economic model (BEPAM) to determine land use under a validated counterfactual scenario with no biofuel policy or with corn ethanol mandate alone to isolate the extent to which expansion of biodiesel production in the US led to the conversion of Conservation Reserve Program (CRP) acres and other noncropland to crop production, over the 2007–2018 period. We find that the land use change intensity of biodiesel ranged from 0.78 to 1.5 million acres per billion gallons in 2018 which is substantially higher than that of corn ethanol, that ranged from 0.57 to 0.75; estimates at the lower end of these ranges are obtained under the assumption that there is no conversion of permanent pastureland to cropland and better supported by model validation than the upper end of these ranges. The land use change elasticity with respect to changes in land rent was more inelastic for biodiesel than for corn ethanol. The largest levels of expansion in cropland were in Iowa, Minnesota, North Dakota, Kansas, Michigan and Mississippi.
Development of a high-resolution top-down model to estimate actual household-level heat pump electricity consumption
Authors: Biscocho Kelsey , Rezqalla Mohammad , Farha Aaron , Boanta Alexandru , Ciez Rebecca E 
Published: May 2023

Abstract
Heat pumps can play an important part in decarbonizing the residential sector due to their use of electricity instead of fossil fuels, and their high efficiency, which often exceeds 100%. However, heat pump performance and energy savings vary with climate and individual household energy usage. Recent studies have used geospatial models to estimate potential heat pump energy consumption across the United States. Yet most studies use generic and oversimplified heat pump models. We contribute to this field with a geospatial model based on manufacturer data and measured test data for 16 different R410A, high efficiency, variable speed compressor heat pumps. Using linear regression, we estimate a market average of COP with respect to ambient temperature. From this, we can identify the variation in efficiency with temperature across this technology class. We also use linear regression to estimate demand for heating and cooling as a function of ambient temperature and household characteristics. We compare the performance of both the predicted energy demand and heat pump efficiency against measured data from a heat pump-equipped house in West Lafayette, Indiana, and find that the model predicts daily heat pump electricity consumption with 27.8% relative error, comparable to other building simulation models. By incorporating high-resolution geospatial data inputs, such top-down models can still maintain a large scope across technologies and diverse climates while increasing spatial and temporal resolution.
On recurrence and transience of some Lévy-type processes in ℝ
Authors: Knopova Victoria 
Published: May 2023

In this note we prove some sufficient conditions for transience and recurrence of a Lévy-type process in

R

\mathbb {R}

, whose generator defined on the test functions is of the form

L
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(
x
)
=

∫

R

(
f
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x
+
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)
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f
(
x
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u

1

|

u

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≤
1

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ν
(
x
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d
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)
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f
∈

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2

(

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.

\begin{equation*} Lf(x) =\int _{\mathbb {R}} \left ( f(x+u)-f(x)- \nabla f(x)\cdot u \mathbb {1}_{|u|\leq 1} \right ) \nu (x,du), \quad f\in C_\infty ^2(\mathbb {R}). \end{equation*}

Here

ν
(
x
,
d
u
)

\nu (x,du)

is a Lévy-type kernel, whose tails are either extended regularly varying or decaying fast enough. For the proof the Foster–Lyapunov approach is used.
Investigating the Shape and Strength of the Relationship Between Maternal Weight Gain and Gestational Age at Delivery in Twin and Singleton Pregnancies
Authors: Dimitris Michelle C , Hutcheon Jennifer A , Platt Robert W , Abrahamowicz Michal , Beauchamp Marie-Eve , Himes Katherine P , Bodnar Lisa M , Kaufman Jay S 
Published: May 2023

AbstractBoth inadequate and excessive maternal weight gain are correlated with preterm delivery in singleton pregnancies, yet this relationship has not been adequately studied in twins. We investigated the relationship between time-varying maternal weight gain and gestational age at delivery in twin pregnancies and compared it with that in singletons delivered in the same study population. We used serial weight measurements abstracted from charts for twin and singleton pregnancies delivered during 1998–2013 in Pittsburgh, Pennsylvania. Our exposure was time-varying weight gain z score, calculated using gestational age–standardized and prepregnancy body mass index–stratified twin- and singleton-specific charts, and our outcome was gestational age at delivery. Our analyses used a flexible extension of the Cox proportional hazards model that allowed for nonlinear and time-dependent effects. We found a U-shaped relationship between weight gain z score and gestational age at delivery among twin pregnancies (lowest hazard of delivery observed at z score = 1.2), which we attributed to increased hazard of early preterm spontaneous delivery among pregnancies with low weight gain and increased hazard of late preterm delivery without labor among pregnancies with high weight gain. Our findings may be useful for updating provisional guidelines for maternal weight gain in twin pregnancies.
PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores
Authors: Holstein Tanja , Kistner Franziska , Martens Lennart , Muth Thilo 
Published: May 2023

Abstract

Motivation
Inferring taxonomy in mass spectrometry-based shotgun proteomics is a complex task. In multi-species or viral samples of unknown taxonomic origin, the presence of proteins and corresponding taxa must be inferred from a list of identified peptides, which is often complicated by protein homology: many proteins do not only share peptides within a taxon but also between taxa. However, the correct taxonomic inference is crucial when identifying different viral strains with high-sequence homology—considering, e.g., the different epidemiological characteristics of the various strains of severe acute respiratory syndrome-related coronavirus-2. Additionally, many viruses mutate frequently, further complicating the correct identification of viral proteomic samples.

Results
We present PepGM, a probabilistic graphical model for the taxonomic assignment of virus proteomic samples with strain-level resolution and associated confidence scores. PepGM combines the results of a standard proteomic database search algorithm with belief propagation to calculate the marginal distributions, and thus confidence scores, for potential taxonomic assignments. We demonstrate the performance of PepGM using several publicly available virus proteomic datasets, showing its strain-level resolution performance. In two out of eight cases, the taxonomic assignments were only correct on the species level, which PepGM clearly indicates by lower confidence scores.

Availability and implementation
PepGM is written in Python and embedded into a Snakemake workflow. It is available at https://github.com/BAMeScience/PepGM.
Cutaneous sarcoma: a review and practical approach to management
Authors: Stoneham Sophie , Hunter Alys , Raahimi Mina , Livesey Amy , Mitchell Charles D , Keohane Stephen 
Published: May 2023

Abstract
Sarcomas arising in the skin are rare but potentially fatal. These tumours originate from mesenchymal cells and can be divided between those that arise in soft tissue and those arising from bone. General guidelines exist for the management of soft-tissue sarcomas; however, there are no specific guidelines for cutaneous sarcomas. Current literature was reviewed for management of seven cutaneous sarcomas including atypical fibroxanthoma, pleomorphic dermal sarcoma, dermal and subcutaneous leiomyosarcoma, dermatofibroma sarcoma protuberans, Kaposi sarcoma, cutaneous angiosarcoma and malignant peripheral nerve sheath tumour. All suspected sarcomas should be discussed in a sarcoma multidisciplinary team meeting. This article is not a clinical guideline but should serve as a practical summary of how these tumours present, how they are recognized histologically, and how best to manage and follow-up patients. The aim is to support clinicians and facilitate the best and most evidence-based standard of care available.
Anthropogenic noise interacts with the predation risk assessment in a free-ranging bird
Authors: Matyjasiak Piotr , Chacińska Patrycja , Książka Piotr 
Published: May 2023

Abstract
Anthropogenic noise can affect a number of behavioral, physiological, and ecological aspects of animals from major taxonomic groups, raising serious conservation concerns. For example, noise pollution impacts communicative behavior and perception of signals, movements and distribution, as well as predator–prey interactions, such as hunting success or predator detection and predation risk assessment. We have carried out an experimental playback study, in which we investigated whether exposure to anthropogenic noise (sound of a tractor) distracts free-ranging barn swallows Hirundo rustica from paying attention to an approaching human “predator” (the “cognitive distraction” hypothesis), or whether noise leads to increased responsiveness to this “predator” (the “increased threat” hypothesis). The subjects were male barn swallows attending their breeding territories during the time when the females were incubating. We found that barn swallow males initiated flight at significantly greater distances to the approaching human “predator” in the noise treatment than during the quiet control trials. These results suggest that anthropogenic noise causes increased vigilance and reactivity rather than a distraction, enabling birds to avoid the “predator” more quickly. We further discuss the mechanism behind the increased alertness in response to noise and contrast the “increased threat” mechanism, usually tested in previous studies, with an alternative “cognitive sensitization” mechanism.
Obefazimod: A First-in-class Drug for the Treatment of Ulcerative Colitis
Authors: Vermeire Séverine , Solitano Virginia , Peyrin-Biroulet Laurent , Tilg Herbert , Danese Silvio , Ehrlich Hartmut , Scherrer Didier , Gineste Paul , d’Agay Laurence , Sands Bruce E 
Published: May 2023

Abstract
Biologic agents and oral small molecules are the mainstays of inflammatory bowel disease [IBD] management. However, an unmet clinical need remains for additional agents with novel mechanism of action which are effective, safe, and disease-modifying; this is due to the substantial proportion of patients who do not respond, lose response, or develop intolerance to currently marketed products. microRNAs [miRNAs] that play a role in the modulation of signal transduction pathways implicated in the development of IBD hold the potential to be used as therapeutic targets. Recently, a novel first-in-class compound, obefazimod, originally conceived as a human immunodeficiency virus [HIV] infection drug, has shown great promise in phase II induction trials for ulcerative colitis [UC] patients. Findings from the maintenance phases of trials showed that long-term obefazimod treatment provides continued improvement in clinical symptoms of disease, with a substantial proportion of patients in clinical remission, and an overall good safety profile. With a novel mechanism of action, obefazimod is an orally available small molecule with anti-inflammatory properties through the specific and selective upregulation of miR-124 expression. The aim of this paper is to critically review the available evidence related to pharmacokinetics and pharmacodynamics, and to discuss the potential clinical implications of this first-in-class oral small molecule.
Tissue plasminogen activator for axillary Impella 5.0 with heparin-induced thrombocytopenia as a treatment of choice for acute Impella thrombosis: a case report
Authors: Merino Elena , Abdelfattah Omar M 
Published: May 2023

AbstractBackgroundPatients with cardiogenic shock requiring temporary support with percutaneous ventricular assist device, such as Impella (Abiomed, Inc.), can develop heparin-induced thrombocytopenia (HIT) which requires use of alternative purge solution anticoagulation. There are limited recommendations on use of anticoagulation other than standard Unfractionated Heparin in 5% dextrose solution.Case summaryThis case describes 69-year-old female who presented with symptoms of decompensated systolic heart failure and was found to be in cardiogenic shock and despite use of inotropes and vasopressors maintained low systolic blood pressure and low mixed venous oxygen saturation which lead to use of axillary Impella 5.0 (Abiomed, Inc.) who developed HIT. Purge solution anticoagulation was switched to Argatroban, but due to increased motor pressures, tissue plasminogen activator (tPA) was successfully used to maintain proper motor pressures. Ultimately, patient was transferred to an outside facility for a transplant evaluation.DiscussionThis case demonstrates successful and safe use of tPA as an alternative purge solution although more data needed to support this finding.
Outcome of Stanford type B dissection in patients with Marfan syndrome
Authors: Yildiz Murat , Nucera Maria , Jungi Silvan , Heinisch Paul Philipp , Mosbahi Selim , Becker Daniel , Siepe Matthias , Schoenhoff Florian 
Published: May 2023

AbstractOBJECTIVESThe aim of this study was to determine the outcome of Stanford type B aortic dissection in patients with Marfan syndrome (MFS) and to evaluate aortic diameters at time of dissection as well as the impact of previous aortic root replacement.METHODSAnalysis of all patients with MFS fulfilling Ghent criteria seen at this institution since 1995 until 2022.RESULTSThirty-six (19%) out of 188 patients with MFS suffered from Stanford type B aortic dissection during the study period. The Mean aortic diameter at the time of dissection was 39.0 mm [95% confidence interval (CI): 35.6–42.3]. The mean pre-dissection diameter (available in 25% of patients) was 32.1 mm (95% CI: 28.0–36.3) and the mean expansion was 19% (95% CI: 11.9–26.2). There was no correlation between age and diameter at the time of dissection (&lt;20, 21–30, 31–40, 41–50, 51–60, &lt;61 years; P = 0.78). Freedom from intervention after dissection was 53%, 44% and 33% at 1, 5 and 10 years. Aortic growth rate in those patients that had to undergo intervention within the 1st year after dissection was 10.2 mm/year (95% CI: 4.4–15.9) compared to 5.8 mm/year (95% CI: 3.3–8.3, P = 0.109) in those thereafter. The mean time between dissection and intervention was 1.8 years (95% CI: 0.6–3.0). While type B dissection seems more frequent after previous elective aortic repair (58% vs 42%), there was no difference between valve-sparing root replacement (VSRR) compared to Bentall procedures [Hazard ratio (HR) for VSRR 0.78, 95% CI: 0.31–2.0, P-value = 0.61]. The mean age of the entire population at the end of follow-up was 42 years (95% CI: 39.2–44.7). The mean follow-up time was 9 years (95% CI: 7.8–10.4).CONCLUSIONSStanford type B dissection in patients with MFS occurs far below accepted thresholds for intervention. Risk for type B dissection is present throughout lifetime and two-thirds of patients need an intervention after dissection. There is no difference in freedom from type B dissection between a Bentall procedure and a VSRR.
Testicular volume in 268 children and adolescents followed-up for childhood obesity—a retrospective cross-sectional study
Authors: Cannarella R , Caruso M , Condorelli R A , Timpanaro T A , Caruso M A , La Vignera S , Calogero A E 
Published: May 2023

AbstractContextPrevalence of obesity in childhood has increased over the past few decades. The impact of obesity and of obesity-related metabolic disorders on testicular growth is unknown.ObjectiveTo evaluate the impact of obesity, hyperinsulinemia, and insulin resistance on testicular volume (TV) in pre-pubertal (&lt;9 years), peri-pubertal (9-14 years), and post-pubertal (14-16 years) periods.MethodsWe collected data on TV, age, standard deviation score (SDS) of the body mass index (BMI), insulin, and fasting glycemia in 268 children and adolescents followed-up for weight control.ResultsPeri-pubertal boys with normal weight had a significantly higher TV compared to those with overweight or obesity. No difference was found in the other age ranges when data were grouped according to BMI. Pre- and post-pubertal children/adolescents with normal insulin levels had significantly higher TV compared to those with hyperinsulinemia. Peri-pubertal boys with hyperinsulinemia had significantly higher TV compared to those with normal insulin levels. Post-pubertal adolescents with insulin resistance had lower TV and peri-pubertal boys had higher TV compared to those without insulin resistance. No difference was found in pre-puberty.ConclusionsCloser control of the body weight and the associated metabolic alterations in childhood and adolescence may maintain testicular function later in life.
Vocational education, general education, and on-the-job learning over the life cycle
Authors: Tobback Ilse , Verhaest Dieter , Baert Stijn , De Witte Kristof 
Published: May 2023

Abstract
We investigate whether vocationally and generally educated individuals differ in their on-the-job learning and how this difference evolves over the career. To this end, we exploit the European Skills and Jobs Survey dataset and rely on instrumental variable estimation. While our descriptive results suggest that workers with a vocational degree experience on average more learning, this conclusion largely changes once endogeneity is taken into account. First, we find that, immediately after graduation, workers with a vocational education are less likely to further improve their skills in their jobs. Second, while this gap in on-the-job learning gradually fades over time, it takes almost a full career to catch up in terms of further on-the-job learning with those with a general degree. Finally, the effects are driven by individuals residing in dual system countries and those with a programme involving workplace learning. We argue that these results are likely explained by a combination of compensating (because vocationally educated obtained their specific skills already during education) and complementary (because general skills lay down a foundation for further learning) effects.
Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae)
Authors: Hutter Carl R , Duellman William 
Published: May 2023

Abstract
An emerging challenge in interpreting phylogenomic data sets is that concatenation and multi-species coalescent summary species tree approaches may produce conflicting results. Concatenation is problematic because it can strongly support an incorrect topology when incomplete lineage sorting (ILS) results in elevated gene-tree discordance. Conversely, summary species tree methods account for ILS to recover the correct topology, but these methods do not account for erroneous gene trees (“EGTs”) resulting from gene tree estimation error (GTEE). Third, site-based and full-likelihood methods promise to alleviate GTEE as these methods use the sequence data from alignments. To understand the impact of GTEE on species tree estimation in Hylidae tree frogs, we use an expansive data set of ∼9,000 exons, introns, and ultra-conserved elements and initially found conflict between all three types of analytical methods. We filtered EGTs using alignment metrics that could lead to GTEE (length, parsimony-informative sites, and missing data) and found that removing shorter, less informative alignments reconciled the conflict between concatenation and summary species tree methods with increased gene concordance, with the filtered topologies matching expected results from past studies. Contrarily, site-based and full-likelihood methods were mixed where one method was consistent with past studies and the other varied markedly. Critical to other studies, these results suggest a widespread conflation of ILS and GTEE, where EGTs rather than ILS are driving discordance. Finally, we apply these recommendations to an R package named PhyloConfigR, which facilitates phylogenetic software setup, summarizes alignments, and provides tools for filtering alignments and gene trees.
Visual processing in the fly, from photoreceptors to behavior
Authors: Currier Timothy A , Pang Michelle M , Clandinin Thomas R 
Published: May 2023

Abstract
Originally a genetic model organism, the experimental use of Drosophila melanogaster has grown to include quantitative behavioral analyses, sophisticated perturbations of neuronal function, and detailed sensory physiology. A highlight of these developments can be seen in the context of vision, where pioneering studies have uncovered fundamental and generalizable principles of sensory processing. Here we begin with an overview of vision-guided behaviors and common methods for probing visual circuits. We then outline the anatomy and physiology of brain regions involved in visual processing, beginning at the sensory periphery and ending with descending motor control. Areas of focus include contrast and motion detection in the optic lobe, circuits for visual feature selectivity, computations in support of spatial navigation, and contextual associative learning. Finally, we look to the future of fly visual neuroscience and discuss promising topics for further study.