bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatically pre-screening patients for the rare disease aromatic l-amino acid decarboxylase deficiency using knowledge engineering, natural language processing, and machine learning on a large EHR population
Authors: Cohen Aaron M , Kaner Jolie , Miller Ryan , Kopesky Jeffrey W , Hersh William 
Published: December 2023

Abstract

Objectives
Electronic health record (EHR) data may facilitate the identification of rare diseases in patients, such as aromatic l-amino acid decarboxylase deficiency (AADCd), an autosomal recessive disease caused by pathogenic variants in the dopa decarboxylase gene. Deficiency of the AADC enzyme results in combined severe reductions in monoamine neurotransmitters: dopamine, serotonin, epinephrine, and norepinephrine. This leads to widespread neurological complications affecting motor, behavioral, and autonomic function. The goal of this study was to use EHR data to identify previously undiagnosed patients who may have AADCd without available training cases for the disease.

Materials and Methods
A multiple symptom and related disease annotated dataset was created and used to train individual concept classifiers on annotated sentence data. A multistep algorithm was then used to combine concept predictions into a single patient rank value.

Results
Using an 8000-patient dataset that the algorithms had not seen before ranking, the top and bottom 200 ranked patients were manually reviewed for clinical indications of performing an AADCd diagnostic screening test. The top-ranked patients were 22.5% positively assessed for diagnostic screening, with 0% for the bottom-ranked patients. This result is statistically significant at P &lt; .0001.

Conclusion
This work validates the approach that large-scale rare-disease screening can be accomplished by combining predictions for relevant individual symptoms and related conditions which are much more common and for which training data is easier to create.
Endogenous reductase activities for the generation of ribitol-phosphate, a CDP-ribitol precursor, in mammals
Authors: Hoshino Shunsuke , Manya Hiroshi , Imae Rieko , Kobayashi Kazuhiro , Kanagawa Motoi , Endo Tamao 
Published: December 2023

Abstract
The core M3 O-mannosyl glycan on α-dystroglycan serves as the binding epitope for extracellular matrix molecules. Defects in core M3 glycans cause congenital muscular dystrophies that are collectively known as dystroglycanopathies. The core M3 glycan contains a tandem D-ribitol-5-phosphate (Rbo5P) structure, which is synthesized by the Rbo5P-transferases fukutin and fukutin-related protein using CDP-ribitol (CDP-Rbo) as a donor substrate. CDP-Rbo is synthesized from CTP and Rbo5P by CDP-Rbo pyrophosphorylase A. However, the Rbo5P biosynthesis pathway has yet to be elucidated in mammals. Here, we investigated the reductase activities toward four substrates, including ribose, ribulose, ribose-phosphate and ribulose-phosphate, to identify the intracellular Rbo5P production pathway and elucidated the role of the aldo-keto reductases AKR1A1, AKR1B1 and AKR1C1 in those pathways. It was shown that the ribose reduction pathway is the endogenous pathway that contributes most to Rbo5P production in HEK293T cells and that AKR1B1 is the major reductase in this pathway.
A Preclinical Blinded Randomized-Controlled Trial Evaluating the Clinical Relevance of Polyp Size Measurement Using a Virtual Scale Endoscope
Authors: Kaufman Daniel , Djinbachian Roupen , Taghiakbari Mahsa , Popescu Crainic Ioana , Haumesser Claire , Abou Khalil Maria , Sidani Sacha , Liu Chen Kiow Jeremy , Panzini Benoit , von Renteln Daniel 
Published: December 2023

Abstract

Background
The virtual scale endoscope (VSE) helps endoscopists measure colorectal polyp size more accurately compared to visual assessment (VA). However, previous studies were not adequately powered to evaluate the sizing of polyps at clinically relevant size thresholds and relative accuracy for size subgroups.

Methods
We created 64 artificial polyps of varied sizes and Paris class morphology, randomly assigned 1:1 to be measured (383 total measurement datapoints with VSE and VA by 6 endoscopists blinded to true size) in a colon model. We added data from two previous trials (480 measurement datapoints). We evaluated for correct classification of polyps into size groups at 3 mm, 5 mm, 10 mm, and 20 mm size thresholds and the relative size measurement accuracy for diminutive polyps (≤5 mm), small polyps (5–9 mm), large polyps at 10–19 mm, and polyps (≥20).

Results
VSE had significantly less size group misclassifications at the 5 mm, and 10 mm thresholds (28 percent vs. 45 percent, P = 0.0159 and 26 percent vs. 44 percent, P = 0.0135, respectively). For the 3 mm and 20 mm thresholds, VSE had lower misclassifications; however, this was not statistically significant (36 percent vs. 46 percent, P = 0.3853 and 38 percent vs. 41 percent, P = 0.2705, respectively). The relative size measurement accuracy was significantly higher for VSE compared to VA for all size subgroups (diminutive (P &lt; 0.01), small polyps (P &lt; 0.01), 10–19 mm (P &lt; 0.01), and ≥20 mm (P &lt; 0.01)).

Conclusion
VSE outperforms VA in categorizing polyps into size groups at the clinically relevant size thresholds of 5 mm and 10 mm. Using VSE resulted in significantly higher relative measurement accuracy for all size subgroups.
Molecular data highlight cryptic diversity and reveal a new species in theSynalpheus brevicarpus(Herrick, 1891) complex (Decapoda: Caridea: Alpheidae) in the Western Atlantic
Authors: Mantelatto Fernando L , França Nielson F C , Cunha Andressa M , Almeida Alexandre O 
Published: December 2023

AbstractRepresentatives of species of alpheid shrimps included in Synalpheus Spence Bate, 1888 exhibit spectacular and distinct behaviors such as eusociality. The wide range of morphological variations in these taxa makes taxonomic understanding difficult. The phylogenetic relationships of the species that comprise the Synalpheus brevicarpus (Herrick, 1891) complex are little known, especially for individuals from South America. Our investigation represents an additional approach to elucidate some aspects of the phylogeny of this species complex. Morphological and molecular evidence resulting from our analyses revealed the existence of a cryptic entity within the S. brevicarpus complex in southeastern Brazil.
Review of surveillance systems for tephritid fruit fly threats in Australia, New Zealand, and the United States
Authors: Kean John M , Manoukis Nicholas C , Dominiak Bernie C 
Published: December 2023

Abstract
Many countries conduct fruit fly surveillance but, while there are guidelines, practices vary widely. This review of some countries in the Pacific region demonstrates the diversity of fruit fly surveillance practices. All utilize 3 parapheromones—trimedlure, cuelure, and methyl eugenol—to trap adult male fruit flies. Some target species are not attracted to these compounds so other attractants such as food-based lures are used in certain areas or circumstances. Lure loading and replacement cycles depend on the target species and the local climate. Malathion and dichlorvos (DDVP) are commonly used toxicants, but not in all countries, and other toxicants are being developed to replace these older-generation pesticides. Jackson and Lynfield are commonly used trap designs but newer designs such as cone and Biotrap are being adopted. Local factors such as chemical registrations and climate affect the choice of trap, lure, dispenser, toxicant, and bait concentration. These choices affect the efficacy of traps, in turn influencing optimal trap deployment in space and time. Most states now follow similar practices around trap inspection, servicing, and data handling, but these processes will be disrupted by emerging automated trap technologies. Ultimately, different practices can be attributed to the unique fruit fly risk profiles faced by each state, particularly the suite of fruit flies already present and those that threaten from nearby. Despite the diversity of approaches, international trade in fruit continues with the assurance that fruit fly surveillance practices evolve and improve according to each country’s risk profile and incursion experience.
Unbalanced optimal transport for full waveform inversion in visco-acoustic media
Authors: Tian Wenbin , Liu Yang , Dong Zilong 
Published: December 2023

Abstract
As a high-precision parameter inversion method, visco-acoustic full waveform inversion (QFWI) is widely used in the inversion of parameters such as velocity and quality factor Q in visco-acoustic media. Conventional QFWI, using the L2 norm as the objective function, is susceptible to face the cycle-skipping problem, especially with inaccurate initial models. Lately, adopting the optimal transportation (OT) distance as the objective function in QFWI (OT-QFWI) has become one of the most promising solutions. In OT-QFWI, converting oscillatory seismic data into a probability distribution that satisfies equal-mass and non-negativity conditions is essential. However, seismic data in visco-acoustic media face challenges in meeting the equal-mass assumption, primarily due to the attenuation effect (amplitude attenuation and phase distortion) associated with the quality factor Q. Unbalanced optimal transportation (UOT) has shown potential in solving equal-mass assumption. It offers the advantage of relaxing equal-mass requirements through entropy regularization. Owing to this advantage, UOT can mitigate the attenuation effect caused by inaccurate quality factor Q during the inversion. Simultaneously, the Sinkhorn algorithm can quickly solve the UOT distance through CUDA programming. Accordingly, we propose a UOT-based QFWI (UOT-QFWI) method to improve the accuracy of two-parameter inversion. The proposed method mitigates the impact of inaccurate quality factor Q by introducing the UOT distance to calculate the objective function, thereby helping to obtain more accurate inverted parameters. Experimental tests on the 1D Ricker wavelet and 2D synthetic model are used to validate the effectiveness and robustness of our proposed method.
Mitogenomic analysis of a late Pleistocene jaguar from North America
Authors: Srigyan Megha , Schubert Blaine W , Bushell Matthew , Santos Sarah H D , Figueiró Henrique Vieira , Sacco Samuel , Eizirik Eduardo , Shapiro Beth 
Published: December 2023

Abstract
The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species’ current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.
Competitor Coupons: A Remedy for Residual Collusion
Authors: Harrington Joseph E 
Published: December 2023

Abstract
There are well-documented episodes of prices remaining at supracompetitive levels even after a cartel was shut down by the competition authority. As long as market conditions remain reasonably stable, collusive prices may still be incentive compatible so the collusive equilibrium could continue after firms are no longer engaging in illicit communications. This situation poses a challenging dilemma: consumer harm persists because of past unlawful conduct but there is no apparent recourse. This paper offers a remedy in the form of coupons. As part of the penalty imposed by the competition authority, each cartel member is required to distribute coupons to its past purchasers. Contrary to their usual form, these coupons can only be used to buy from a firm’s competitors. I show how this temporary intervention can help destabilize collusion and restore competition.
War-induced energy insecurity in Europe: what role for liquefied natural gas after the Russia’s invasion of Ukraine?
Authors: Soliman Hunter Tina 
Published: December 2023

Abstract
This article addresses the issue of energy insecurity in Europe arising from the Russia–Ukraine war, and Europe’s decision to ‘consciously uncouple’ from its use and reliance on Russian gas. After considering the cause and consequences of EU reliance on Russian gas, this article considers the role of floating storage and regassification units (FSRUs), vessels designed to store liquefied natural gas (LNG) until needed and then to regassify the LNG directly into the gas pipeline distribution network. This article considers FSRUs in general, and the experiences of Finland and Germany as they diversify away from Russian gas. It also considers the contribution of Croatia’s Krk Terminal in Croatian and Balkan energy security. Finally, this article considers legal issues arising from the rapid deployment of FSRUs, especially in countries with no previous experience of such hazardous facilities.
Update of the Shakespeare First Folio Census
Authors: James West Anthony 
Published: December 2023

Abstract
This update of the Shakespeare First Folio Census (2003) records all sales and discoveries of First Folios since 2000. Each of the seven ‘new’ Folios, ones that did not appear among the 228 Folios in the Census, is given a new ‘West’ number, accompanied by information on provenance and seller, auctioneer or bookseller, and buyer and price, plus comments as appropriate. There are now 235 extant First Folios in the world, each with an identifying number, and the precise location is known of almost all. It is likely there are more First Folios lurking somewhere. The two addenda may help to find them: Pursuing Leads to ‘New’ Folios; and Some Targets for First Folio Hunters.
Criminogenic Needs and Legal Problem Severity Among Legal System Involved Veterans
Authors: Bowdring Molly A , Macia Kathryn S , Shaffer Paige M , Smelson David , Blonigen Daniel M 
Published: December 2023

ABSTRACT

Background
Many veterans seeking behavioral health services have history of criminal–legal involvement. Research on criminogenic needs of legal system involved veterans is burgeoning. However, most research has relied on cross-sectional examinations and the vast majority of prior work has focused assessment on just one criminogenic need per study.

Methods
The present study evaluated seven key criminogenic needs of legal system involved veterans (N = 341) enrolled in one of three U.S. Veterans Health Administration residential behavioral health treatment programs. Criminogenic needs and legal problem severity were assessed at baseline, and at 6 months and 12 months post-baseline. Directionality of associations between participants’ criminogenic needs and legal problem severity was examined using latent change score models.

Results
Results revealed having more antisocial associates at a previous timepoint was associated with greater subsequent improvements in legal problem severity ($\beta $=−0.01, P &lt; 0.02) and greater improvements in legal problem severity predicted greater subsequent improvements in alcohol problem severity ($\beta $=0.13, P &lt; 0.01).

Conclusions
In one of the most comprehensive single-study assessments of criminogenic needs among a sample of legal system involved veterans, results highlight links between antisocial associates and alcohol problem severity with legal problem severity.
Young Man With Primary Mucinous Cell Carcinoma of the Eyelid: 36 Month Follow Up
Authors: Alazawi Sama S , Katana Vienna G 
Published: December 2023

ABSTRACT
Primary cutaneous mucinous carcinoma (PCMC) is a malignant adnexal tumor that masquerades as a benign periocular lesion. We present a case of a 29-year-old male with an eyelid PCMC misdiagnosed as a chalazion. He underwent Mohs microscopic surgery for definitive treatment, with no recurrence at his 36 month follow up. Given the rarity and poorer prognosis in younger patients, a high index of suspicion is crucial for biopsying periocular lesions that fail conservative therapy.
When Patient Portals Break Bad News
Authors: Iodice Eleanor , Penick Emily , Winkler Stuart S 
Published: December 2023

ABSTRACT
Electronic patient portals facilitate communication between providers and patients, but they can complicate the art of breaking bad news. Nearly half of oncology patients will view their diagnosis on a patient portal before speaking with a provider. Physicians and advanced practice providers receive training on how to deliver bad news in person and over the telephone. This is done in an empathetic and supportive manner. The patient’s emotions are acknowledged, and questions are answered. While surveys of patients suggest that most people prefer an in-person or telephone conversation to receive bad news, the electronic portal can undermine this delicate conversation when oncology reports are prematurely accessed. Military providers should be aware of the impact electronic portal usage may have on patients. We provide suggestions for providers to adjust their practice accordingly, such as warning patients about their early access to results prior to a planned follow-up visit. We also suggest that MHS GENESIS, the electronic health record for the Military Health System (MHS), allows for sensitive reports to be released to patients after the results are discussed rather than automatically after 36 hours. Electronic portals streamline patient–provider communication and increase transparency; however, we should consider that the task of delivering bad news was never meant for computers.
Mitigating astrometric bias in barycentric correction with PEXO
Authors: Rui Yicheng , Feng Fabo 
Published: December 2023

ABSTRACT
Extremely precise radial velocity is essential for the detection of sub-m s−1 radial velocity of stars induced by Earth-like planets. Although modelling of the barycentric correction of radial velocity could achieve 1 mm s−1 precision, the input astrometry could be biased due to non-linear motions of stars caused by companions. To account for astrometry induced bias in barycentric correction, we correct for astrometric bias by minimizing the scatter of reduced RV data with Precise EXOplanetology (PEXO). In particular, we apply this method to the barycentric correction for 266 stars from HARPS data archive. We find that the RV scatter for eight targets are significantly reduced due to correction of astrometric bias. Among these targets, two targets exhibit bias caused by known massive companions, while for the remaining six targets, the bias could be attributed to unknown companions or Gaia systematics. Furthermore, 14 targets have an astrometry induced annual RV variation higher than 0.05  m s−1, and 10 of them are closer than 10 pc. We show the results of Barnard’s star as an example, and find that an annual RV bias of 10 cm s−1 is mitigated by replacing BarCor by PEXO as the barycentric correction code. Our work demonstrates the necessity of astrometric bias correction and the utilization of barycentric correction code within a relativistic framework in high-precision RV for the detection of Earth-like planets.
The impact of gas accretion and AGN feedback on the scatter of the mass–metallicity relation
Authors: Yang Nancy , Scholte Dirk , Saintonge Amélie 
Published: December 2023

ABSTRACT
The gas-phase metallicity of galaxies encodes important information about galaxy evolution processes, in particular star formation, feedback, outflows, and gas accretion, the relative importance of which can be extracted from systematic trends in the scatter of the mass–metallicity relation (MZR). Here, we use a sample of low-redshift (0.02 &lt; z &lt; 0.055) galaxies from SDSS to investigate the nature of the scatter around the MZR, the observables and physical processes causing it, and its dependence on galaxy mass. We use cold gas masses inferred from optical emission lines using the technique of Scholte & Saintonge (2023) to confirm that at fixed stellar mass, metallicity and gas mass are anticorrelated, but only for galaxies up to M* = 1010.5 M⊙. In that mass regime, we find a link between the offset of a galaxy from the MZR and halo mass, using the amplitude of the two-point correlation function as a proxy for halo mass; at fixed stellar mass, the most gas-poor galaxies reside in the most massive haloes. This observation is consistent with changes in gas accretion rates onto galaxies as a function of halo mass, with environmental effects acting on satellite galaxies also contributing. At higher stellar masses, the scatter of the MZR does no longer correlate with gas or halo mass. Instead, there is some indication of a link with AGN activity, as expected from models and simulations that metallicity is set by the interplay between gas in- and outflows, star formation, and AGN feedback, shaping the MZR and its scatter.
On the detectability of interstellar diaminomethane ((NH2)2CH2)
Authors: Watrous Alexandria G , Westbrook Brent R , Fortenberry Ryan C 
Published: December 2023

ABSTRACT
The recent synthesis of diaminomethane ((NH2)2CH2) under simulated interstellar conditions implies that this molecule is likely present in the interstellar medium (ISM), and this work provides the highly accurate quantum chemically computed rotational constants and IR frequencies for comparison to experiment that may aid in its potential future detection. This simplest geminal diamine of prebiotic note has a transition for its ν18 fundamental frequency at 702.5 cm−1 (14.23 μm) with an intensity on level with that of the antisymmetric stretch in carbon dioxide. Additionally, its 1.72 D dipole moment for the most stable C2v conformer should make it detectable with radiotelescopes as well. The C2 conformer may also be detectable in similar regions where the C2v form is present, but only warmer or higher-energy regions will allow for possible observation of the C1 conformer. In any case, rotational constants for these other two conformers are also provided in addition to the full set of fundamental vibrational frequencies for the C2v conformer. These data will assist with further laboratory classification and possible interstellar detection of this prebiotic molecule.