bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vancomycin AUC values estimated with trough-only data: Accuracy in an adult academic medical center population
Authors: Arensman Hannan Kellie N , Rivera Christina G , Fewel Nathan 
Published: December 2022

AbstractPurposeVancomycin area under the concentration-time curve (AUC) can be calculated using steady-state serum peak and trough concentrations; however, compared to traditional trough-only monitoring, this approach requires an additional blood sample. Recently published data demonstrated vancomycin AUC estimations using trough-only data with a volume of distribution (Vd) model incorporating age and actual body weight were reasonably accurate and precise in a veteran population. This study sought to extend these methods to a Mayo Clinic adult population.MethodsA retrospective, observational cohort of adult patients with documented steady-state vancomycin peak and trough concentrations was evaluated. Vancomycin AUCs were estimated using trough-only data, and 4 Vd models were assessed for accuracy and precision. Estimated AUCs were compared to AUCs calculated using 1-compartment intermittent infusion equations and steady-state peak and trough (“peak-trough”) data.ResultsThe study population (N = 95) was 46% female, with a median age of 59 years and a median weight of 97 kg. Using the VancoPK equation Vd = 0.29 (age in y) + 0.33 (actual weight in kg) + 11, the mean peak-trough and estimated trough-only AUC were 533 and 534, respectively, with a correlation of 0.936. The root mean square error was 47.7, meaning about 95% of AUCs were within 95 mg · h/L of peak-trough AUCs.ConclusionsAccuracy and precision of Vancomycin AUC estimations using trough-only data and the described Vd model were demonstrated in a Mayo Clinic cohort. Targeting an estimated AUC of 500 mg · h/L using the VancoPK model would likely result in an actual AUC within 400 to 600 mg · h/L.
Evaluating reduction in medical costs associated with pharmacists’ presence in the emergency department using a novel cost avoidance framework
Authors: Poremba Matthew , Champa Kelsey , Reichert Erin 
Published: December 2022

Abstract

Purpose
The purpose of this study was to evaluate the cost avoidance associated with emergency medicine pharmacist (EMP) presence in the emergency department (ED) using a novel cost avoidance framework.

Summary
This single-center, retrospective, observational study examined EMP interventions from November 1, 2021, through March 31, 2022. EMPs prospectively selected up to 10 shifts in which to log interventions during the study period. Interventions were categorized into 25 cost avoidance categories, 10 of which incorporated recently proposed probability variables. All categories were organized into 4 broad cost avoidance domains, including resource utilization, individualization of patient care, adverse drug event prevention, and hands-on care. During the study period, 894 interventions were logged, which accounted for $143,132 in cost avoidance (lower probability value of $124,186, upper probability value of $168,858), with a median cost avoidance per shift of $1,671 (interquartile range, $1,025 to $2,451). On the basis of 240 shifts, the estimated annual total cost avoidance per pharmacist was extrapolated to be $401,040.

Conclusion
While the mean cost avoidance of $161.10 per intervention observed in our study was less than that in prior cost avoidance studies due to the conservative and potentially more realistic estimates used, implementation of this cost avoidance framework still showed substantial cost avoidance associated with EMP presence in the ED.
DMPPred: a tool for identification of antigenic regions responsible for inducing type 1 diabetes mellitus
Authors: Kumar Nishant , Patiyal Sumeet , Choudhury Shubham , Tomer Ritu , Dhall Anjali , Raghava Gajendra P S 
Published: December 2022

AbstractThere are a number of antigens that induce autoimmune response against β-cells, leading to type 1 diabetes mellitus (T1DM). Recently, several antigen-specific immunotherapies have been developed to treat T1DM. Thus, identification of T1DM associated peptides with antigenic regions or epitopes is important for peptide based-therapeutics (e.g. immunotherapeutic). In this study, for the first time, an attempt has been made to develop a method for predicting, designing, and scanning of T1DM associated peptides with high precision. We analysed 815 T1DM associated peptides and observed that these peptides are not associated with a specific class of HLA alleles. Thus, HLA binder prediction methods are not suitable for predicting T1DM associated peptides. First, we developed a similarity/alignment based method using Basic Local Alignment Search Tool and achieved a high probability of correct hits with poor coverage. Second, we developed an alignment-free method using machine learning techniques and got a maximum AUROC of 0.89 using dipeptide composition. Finally, we developed a hybrid method that combines the strength of both alignment free and alignment-based methods and achieves maximum area under the receiver operating characteristic of 0.95 with Matthew’s correlation coefficient of 0.81 on an independent dataset. We developed a web server ‘DMPPred’ and stand-alone server for predicting, designing and scanning T1DM associated peptides (https://webs.iiitd.edu.in/raghava/dmppred/).
YaHS: yet another Hi-C scaffolding tool
Authors: Zhou Chenxi , McCarthy Shane A , Durbin Richard 
Published: December 2022

Abstract

Summary
We present YaHS, a user-friendly command-line tool for the construction of chromosome-scale scaffolds from Hi-C data. It can be run with a single-line command, requires minimal input from users (an assembly file and an alignment file) which is compatible with similar tools and provides assembly results in multiple formats, thereby enabling rapid, robust and scalable construction of high-quality genome assemblies with high accuracy and contiguity.

Availability and implementation
YaHS is implemented in C and licensed under the MIT License. The source code, documentation and tutorial are available at https://github.com/sanger-tol/yahs.

Supplementary information
Supplementary data are available at Bioinformatics online.
Hedgehog signaling regulates Wolffian duct development through the primary cilium
Authors: Alves Maíra Bianchi Rodrigues , Girardet Laura , Augière Céline , Moon Kyeong Hye , Lavoie-Ouellet Camille , Bernet Agathe , Soulet Denis , Calvo Ezequiel , Teves Maria E , Beauparlant Charles Joly , Droit Arnaud , Bastien Alexandre , Robert Claude , Bok Jinwoong , Hinton Barry T , Belleannée Clémence 
Published: December 2022

AbstractPrimary cilia play pivotal roles in embryonic patterning and organogenesis through transduction of the Hedgehog signaling pathway (Hh). Although mutations in Hh morphogens impair the development of the gonads and trigger male infertility, the contribution of Hh and primary cilia in the development of male reproductive ductules, including the epididymis, remains unknown. From a Pax2Cre; IFT88fl/fl knock-out mouse model, we found that primary cilia deletion is associated with imbalanced Hh signaling and morphometric changes in the Wolffian duct (WD), the embryonic precursor of the epididymis. Similar effects were observed following pharmacological blockade of primary cilia formation and Hh modulation on WD organotypic cultures. The expression of genes involved in extracellular matrix, mesenchymal-epithelial transition, canonical Hh and WD development was significantly altered after treatments. Altogether, we identified the primary cilia-dependent Hh signaling as a master regulator of genes involved in WD development. This provides new insights regarding the etiology of sexual differentiation and male infertility issues.
Trends in treatment and outcomes of atrial fibrillation during 2007–17 in Finland
Authors: Teppo Konsta , Airaksinen K E Juhani , Jaakkola Jussi , Halminen Olli , Linna Miika , Haukka Jari , Putaala Jukka , Mustonen Pirjo , Kinnunen Janne , Hartikainen Juha , Aro Aapo L , Lehto Mika 
Published: December 2022

Abstract

Aims
Guidelines on the management of atrial fibrillation (AF) have evolved significantly during the past two decades, but the concurrent developments in real-life management and prognosis of AF are unknown. We assessed trends in the treatment and outcomes of patients with incident AF between 2007 and 2017.

Methods and results
The registry-based nationwide FinACAF (Finnish AntiCoagulation in Atrial Fibrillation) cohort covers all patients with AF in Finland from all levels of care. We determined the proportion of patients who were treated with oral anticoagulants (OACs) or rhythm control therapies, experienced an ischaemic stroke or bleeding event requiring hospitalization, or died within 1-year follow-up after AF diagnosis. We identified 206 909 patients (mean age 72.6 years) with incident AF. During the study period, use of OACs increased from 43.6 to 76.3%, and the increase was most evident in patients with at least moderate stroke risk. One-year mortality decreased from 13.3 to 10.6%, and the ischaemic stroke rate from 5.3 to 2.2%. The prognosis especially improved in patients over 75 years of age. Concurrently, a small increase in major bleeding events was observed. Use of catheter ablation increased continuously over the study period, but use of other rhythm-control therapies decreased after 2013.

Conclusion
Stroke prevention with OACs in patients with incident AF improved considerably from 2007 to 2017 in Finland. This development was accompanied by decreasing 1-year mortality and the reduction of the ischaemic stroke rate by more than half, particularly among elderly patients, whereas there was only slight increase in severe bleeding events.
Driving under the Influence of Amphetamine: Analytical Evaluation of Illegal or Prescription Drug Intake Using Chiral UHPLC–MS-MS
Authors: Nielsen Marie Katrine Klose , Andersen Nina Zacho , Rasmussen Brian Schou , Johansen Sys Stybe 
Published: December 2022

AbstractDifferentiation between consumption of illegal and prescription drugs remains an important aspect in forensic toxicology. While illicit amphetamine is most often racemic, the medicinal drugs marketed in Denmark for the treatment of attention-deficit hyperactivity disorder contain the pure (S)-enantiomer or a prodrug thereof. In this study, we present a simple and efficient analytical workflow to provide information about the origin of amphetamine consumed in forensic cases concerning driving under the influence of drugs (DUID). Following quantification of amphetamine and methamphetamine using our conventional multi-target ultra-high performance liquid chromatography–tandem mass spectrometry method, determination of (R)- and (S)-amphetamine was performed by reinjecting the sample extract on a Phenomenex LUX® AMP chiral column using the same analytical instrument and mobile phases. Chiral separation was performed isocratic within a run time of 6 min. The analytical workflow was applied to blood samples from 5,248 suspected DUID cases within a 2-year period. Amphetamine was detected in 18.7% of the samples, of which both enantiomers were detected in 89.5% of the cases, indicating the consumption of illegal racemic amphetamine. In 6.1% of the positive cases, both amphetamine and methamphetamine were detected, indicating either co-consumption of both amphetamines or consumption of methamphetamine. In the remaining 4.4%, only (S)-amphetamine was detected indicating the consumption of prescription drugs containing (S)-amphetamine or a prodrug thereof. Implementation of a simple and rapid chiral method in the conventional analytical workflow for routine forensic casework proved to be an efficient way to elucidate whether a positive amphetamine result originates from illegal or prescription drug consumption, without increasing turnaround time nor costs to any significant extent, as no additional sample preparation was required.
Velocity-coherent substructure in TMC-1: inflow and fragmentation
Authors: Smith Simon E T , Friesen Rachel , Marchal Antoine , Pineda Jaime E , Caselli Paola , Chen Michael Chun-Yuan , Choudhury Spandan , Di Francesco James , Ginsburg Adam , Kirk Helen , Matzner Chris , Punanova Anna , Scibelli Samantha , Shirley Yancy 
Published: December 2022

ABSTRACT
Filamentary structures have been found nearly ubiquitously in molecular clouds and yet their formation and evolution is still poorly understood. We examine a segment of Taurus Molecular Cloud 1 (TMC-1) that appears as a single, narrow filament in continuum emission from dust. We use the Regularized Optimization for Hyper-Spectral Analysis (ROHSA), a Gaussian decomposition algorithm that enforces spatial coherence when fitting multiple velocity components simultaneously over a data cube. We analyse HC5N (9–8) line emission as part of the Green Bank Ammonia Survey and identify three velocity-coherent components with ROHSA. The two brightest components extend the length of the filament, while the third component is fainter and clumpier. The brightest component has a prominent transverse velocity gradient of 2.7 ± 0.1 km s−1 pc−1 that we show to be indicative of gravitationally induced inflow. In the second component, we identify regularly spaced emission peaks along its length. We show that the local minima between pairs of adjacent HC5N peaks line up closely with submillimetre continuum emission peaks, which we argue is evidence for fragmentation along the spine of TMC-1. While coherent velocity components have been described as separate physical structures in other star-forming filaments, we argue that the two bright components identified in HC5N emission in TMC-1 are tracing two layers in one filament: a lower density outer layer whose material is flowing under gravity towards the higher density inner layer of the filament.
A theoretical study of the time lags due to Comptonization and the constraints on the X-ray corona in AGNs
Authors: Zhang W , Papadakis I E , Dovčiak M , Bursa M , Karas V 
Published: December 2022

ABSTRACT
We study the Fourier time lags due to the Comptonization of disc-emitted photons in a spherical, uniform, and stationary X-ray corona, which located on the rotational axis of the black hole. We use monk, a general relativistic Monte Carlo radiative transfer code, to calculate Compton scattering of photons emitted by a thin disc with a Novikov–Thorne temperature profile. We find that the model time lags due to Comptonization remain constant up to a characteristic frequency and then rapidly decrease to zero at higher frequencies. We provide equations that can be used to determine the time lags and cross-spectra for a wide range of values for the corona radius, temperature, optical depth, height, and for various accretion rates and black hole masses. We also provide an equation for the X-ray luminosity of a single corona, as a function of its characteristics and location above the disc. Remarkably, the observed X-ray time lags of nearby, bright active galaxies can be successfully reproduced by inverse Comptonization process of multiple dynamic coronae.
The role of the drag force in the gravitational stability of dusty planet forming disc – I. Analytical theory
Authors: Longarini Cristiano , Lodato Giuseppe , Bertin Giuseppe , Armitage Philip J 
Published: December 2022

ABSTRACT
Recent observations show that planet formation is already underway in young systems, when the protostar is still embedded into the molecular cloud and the accretion disc is massive. In such environments, the role of self-gravity (SG) and gravitational instability (GI) is crucial in determining the dynamical evolution of the disc. In this work, we study the dynamical role of drag force in self-gravitating discs as a way to form planetesimals in early protoplanetary stages. We obtain the dispersion relation for density-wave perturbations on a fluid composed of two phases (gas and dust) interacting through the common gravitation field and the mutual drag force, and we find that the stability threshold is determined by three parameters: the local dust-to-gas density ratio, the dust relative temperature, and the relevant Stokes number. In a region of parameters space, where young protoplanetary discs are likely to be found, the instability can be dust driven, occurring at small wavelengths. In this regime, the Jeans mass is much smaller than the one predicted by the standard GI model. This mechanism can be a viable way to form planetary cores in protostellar discs, since their predicted mass is about ∼10 M⊕.
Impact of HAC evolution on the formation of small hydrocarbons in the Orion Bar and the Horsehead PDRs
Authors: Murga M S , Vasyunin A I , Kirsanova M S 
Published: December 2022

ABSTRACT
We study evolution of hydrogenated amorphous carbon (HAC) grains under harsh UV radiation in photodissociation regions (PDRs) near young massive stars. Our aim is to evaluate the impact of the HAC grains on formation of observed small hydrocarbons: C2H, C2H2, C3H+, C3H, C3H2, C4H, in PDRs. We developed a microscopic model of the HAC grains based on available experimental results. The model includes processes of photo and thermo-desorption, accretion of hydrogen and carbon atoms and subsequent formation of carbonaceous mantle on dust surface. H2, CH4, C2H2, C2H4, C2H6, C3H4, C3H6, C3H8 are considered as the main fragments of the HAC photodestruction. We simulated evolution of the HAC grains under the physical conditions of two PDRs, the Orion Bar and the Horsehead nebula. We estimated the production rates of the HAC’ fragments in gas phase chemical reactions and compared them with the production rates of fragments due to the HAC destruction. The latter rates may dominate under some conditions, namely, at AV = 0.1 in both PDRs. We coupled our model with the gas-grain chemical model MONACO and calculated abundances of observed small hydrocarbons. We conclude that the contribution of the HAC destruction fragments to chemistry is not enough to match the observed abundances, although it increases the abundances by several orders of magnitude in the Orion Bar at AV = 0.1. Additionally, we found that the process of carbonaceous mantle formation on dust surface can be an inhibitor for the formation of observed small hydrocarbons in PDRs.
Baryon pasting algorithm: halo-based and particle-based pasting methods
Authors: Osato Ken , Nagai Daisuke 
Published: December 2022

ABSTRACT
We present a fast methodology to produce mock observations of the thermal and kinetic Sunyaev–Zel’dovich (SZ) effects based on the dark matter only N-body simulations coupled with the analytic intracluster medium model. The methods employ two different approaches: halo-based pasting (HP) and particle-based pasting (PP). The former pastes gas density and pressure on to haloes and requires only a halo catalogue, and the latter considers the contribution from field particles as well, i.e. particles that do not belong to any haloes and thus utilize the full particle information. Therefore, the PP algorithm incorporates secondary effects beyond the HP algorithm: asphericity of haloes and contribution from diffuse gas. In particular, such a diffuse component is the dominant source of the kinetic SZ effect. As validation of our methods, we have produced 108 all-sky maps with HP and 108 flat-sky maps, which cover $5 \times 5 \, \mathrm{deg}^2$ with both HP and PP, and measured power spectra of the maps. Our method can produce a mock map within a few hours, even for all-sky coverage with a parallel computational environment. The power spectra of HP maps are consistent with the halo model prediction of the thermal SZ effect. On the other hand, the power spectra of PP maps are suppressed due to the halo asphericity but can reproduce better the theoretical prediction for the kinetic SZ effect. We discuss the utility of baryon-pasted mock SZ maps for estimating the covariance matrix of SZ statistics and modelling the selection and projection effects for cluster cosmology.
Radial velocity confirmation of a hot super-Neptune discovered by TESS with a warm Saturn–mass companion
Authors: Knudstrup E , Gandolfi D , Nowak G , Persson C M , Furlan E , Livingston J , Matthews E , Lundkvist M S , Winther M L , Rørsted J L , Albrecht S H , Goffo E , Carleo I , Deeg H J , Collins K A , Narita N , Isaacson H , Redfield S , Dai F , Hirano T , Akana Murphy J M , Beard C , Buchhave L A , Cary S , Chontos A , Crossfield I , Cochran W D , Conti D , Dalba P A , Esposito M , Fajardo-Acosta S , Giacalone S , Grunblatt S K , Guerra P , Hatzes A P , Holcomb R , Horta F G , Howard A W , Huber D , Jenkins J M , Kabáth P , Kane S , Korth J , Lam K W F , Lester K V , Matson R , McLeod K K , Orell-Miquel J , Murgas F , Palle E , Polanski A S , Ricker G , Robertson P , Rubenzahl R , Schlieder J E , Seager S , Smith A M S , Tenenbaum P , Turtelboom E , Vanderspek R , Weiss L , Winn J 
Published: December 2022

ABSTRACT
We report the discovery and confirmation of the planetary system TOI-1288. This late G dwarf harbours two planets: TOI-1288 b and TOI-1288 c. We combine TESS space-borne and ground-based transit photometry with HARPS-N and HIRES high-precision Doppler measurements, which we use to constrain the masses of both planets in the system and the radius of planet b. TOI-1288 b has a period of $2.699835^{+0.000004}_{-0.000003}$ d, a radius of 5.24 ± 0.09 R⊕, and a mass of 42 ± 3 M⊕, making this planet a hot transiting super-Neptune situated right in the Neptunian desert. This desert refers to a paucity of Neptune-sized planets on short period orbits. Our 2.4-yr-long Doppler monitoring of TOI-1288 revealed the presence of a Saturn–mass planet on a moderately eccentric orbit ($0.13^{+0.07}_{-0.09}$) with a minimum mass of 84 ± 7 M⊕ and a period of $443^{+11}_{-13}$ d. The five sectors worth of TESS data do not cover our expected mid-transit time for TOI-1288 c, and we do not detect a transit for this planet in these sectors.
Living without pain. Case series of patients with hereditary sensory and autonomic neuropathies in a Canadian tertiary care centre
Authors: Reddi Renitha , Horvath Gabriella A 
Published: December 2022

Abstract

Background
Hereditary sensory and autonomic neuropathies (HSANs) are a group of heterogeneous genetic disorders presenting predominantly with sensory and autonomic dysfunction. They are a diverse group of diseases of the peripheral nervous system characterized by profound distal sensory loss and various autonomic and motor disturbances.

Objectives
The primary objective of this study was to describe the clinical presentation of children with HSAN to paediatricians. We present clinical features and genetic etiology of patients with HSAN followed in a Canadian tertiary paediatric centre, including suggestions for their monitoring, management, and long-term follow-up.

Methods
A retrospective chart review of all patients with HSAN followed from the years 2000 through 2021 was performed. Collected data consisted of patients’ demographics, clinical characteristics, imaging, and management.

Results
Eight patients were included. The average age at diagnosis was 3.19 ± 2.83 years. Insensitivity to pain (100%), dysautonomia (100%), global development delay (87.5%), emesis (62.5%), and self-injury (62.5%) were the most prevalent manifestations of HSAN. The most common co-morbidities were gastroesophageal reflux disease (50%), obstructive sleep apnea (37.5%), attention-deficit hyperactivity disorder (37.5%), and iron deficiency (37.5%). Management was multi-disciplinary, involving neurologists, orthopeds, developmental paediatricians, sleep specialists, and psychiatrists.

Conclusion
HSANs are a diverse group of diseases, characterized by profound distal sensory loss, acral mutilations, and variable autonomic disturbances. It is important to recognize the diagnosis in the paediatrician’s office in order to set up surveillance and prevent complications.