bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association between pill mill legislation and neonatal abstinence syndrome
Authors: Anwar Tahiya , Jayawardhana Jayani 
Published: December 2021

Abstract

Objectives
Neonatal abstinence syndrome (NAS) is a drug withdrawal syndrome in newborns who were primarily been exposed to drugs such as opioids in the mothers’ womb. The NAS rate in the USA has increased over the past decade. With rising opioid use and opioid overdose deaths, many states adopted various policies to combat the opioid epidemic, including the pill mill legislation. However, its effect on NAS is not evident. This study examines the association between pill mill legislation and NAS rate in the USA.

Methods
The study utilizes state-level hospital discharge data from Healthcare Cost and Utilization Project’s (HCUP) Fast Stats database from 2008 to 2018, along with state-level socio-demographic and opioid-related health policy data. Analysis was conducted using a difference-in-differences regression approach.

Key findings
The results indicate that pill mill legislation is associated with 4 additional incidents of NAS cases per 1000 newborn hospitalizations (P &lt; 0.05), and 6.5 additional incidents of NAS cases per 1000 newborn hospitalizations among Medicaid payers (P &lt; 0.05) in states with pill mill legislation compared with states without the legislation. Moreover, the results indicate that states with prescription drug monitoring programmes (PDMP) are experiencing lower incidents of NAS cases overall (P &lt; 0.01), and among Medicaid and privately insured populations (P &lt; 0.05) in comparison with states without PDMPs.

Conclusions
These findings indicate that pill mill legislation has not been effective in reducing NAS rates in the USA. A comprehensive policy approach targeting opioid use among pregnant women may be needed to effectively reduce NAS rates in the USA.
The Impact of Having a Child With Special Healthcare Needs on Length of Military Service
Authors: Perkins Elizabeth M , Sorensen Ian , Susi Apryl , Hisle-Gorman Elizabeth 
Published: December 2021

ABSTRACT

Introduction
In 2010, the National Survey of Children with Special Healthcare Needs revealed that parents of children with special healthcare needs (CSHCN) report employment decisions are influenced by healthcare coverage needs. The U.S. military healthcare system arguably offers service member parents of CSHCN with the most comprehensive, inexpensive, long-term healthcare in the country—potentially increasing their incentive to remain in the military. This study explored the effect of having a CSHCN on the length of parental military service.

Materials and Methods
A retrospective cohort was formed using the Military Health System database from 2008 to 2018. Included children were &lt;10 years in 2010 and received ≥1 year of military healthcare between 2008 and 2010. The Pediatric Medical Complexity Algorithm categorized children as having special healthcare needs via ICD 9/10 codes as having complex chronic (C-CD), non-complex chronic (NC-CD), or no chronic disease (CD). Families were classified by the child with the most complex healthcare need. Duration of military healthcare eligibility measured parental length of service (LOS). ANOVA and linear regression analysis compared LOS by category. Logistic regression determined odds of parental LOS lasting the full 8-year study length. Adjusted analyses controlled for child age and sex, and military parent sex, rank, and marital status.

Results
Over 1.45 million children in 915,584 families were categorized as per the algorithm. Of individual children included, 292,050 (20.1%) were CSHCN including those with complex chronic and non-complex chronic conditions. After grouping by family, 80,909 (8.8%) families had a child/children with C-CD (mean LOS 6.39 years), 170,787 (18.7%) families had a child/children with NC-CD (mean LOS 6.41 years), and 663,888 (72.5%) families had children with no CD (mean LOS 5.7 years). In adjusted analysis, parents of children with C-CD and NC-CD served 0.4 [0.37-0.42] and 0.33 [0.31-0.34] years longer than parents of children with no CD; odds of parents serving for the full study period were increased 33% (1.33 [1.31-1.36]) in families of children with C-CD and 27% (1.27 [1.26-1.29]) in families of children with NC-CD.

Conclusions
Findings indicate that military parents of CSHCN serve longer military careers than parents of children with no chronic conditions. Continued provision of free, high-quality healthcare coverage for dependent children may be important for service member retention. Retaining trained and experienced service members is key to ensuring a ready and lethal U.S. military.
Onboard dynamic image exposure control for the Star–Planet Activity Research CubeSat (SPARCS)
Authors: Ramiaramanantsoa Tahina , Bowman Judd D , Shkolnik Evgenya L , Loyd R O Parke , Ardila David R , Jewell April , Barman Travis , Basset Christophe , Beasley Matthew , Cheng Samuel , Gamaunt Johnathan , Gorjian Varoujan , Hennessy John , Jacobs Daniel , Jensen Logan , Knapp Mary , Llama Joe , Meadows Victoria , Nikzad Shouleh , Peacock Sarah , Scowen Paul , Swain Mark R 
Published: December 2021

ABSTRACT
The Star–Planet Activity Research CubeSat (SPARCS) is a 6U CubeSat under development to monitor the flaring and chromospheric activity of M dwarfs at near-ultraviolet (NUV) and far-ultraviolet (FUV) wavelengths. The spacecraft hosts two UV-optimized delta-doped charge-coupled devices fed by a 9-cm telescope and a dichroic beam splitter. A dedicated science payload processor performs near-real-time onboard science image processing to dynamically change detector integration times and gains to reduce the occurrence of pixel saturation during strong M dwarf flaring events and provide adequate flare light-curve structure resolution while enabling the detection of low-amplitude rotational modulation. The processor independently controls the NUV and FUV detectors. For each detector, it derives control updates from the most recent completed exposure and applies them to the next exposure. The detection of a flare event in the NUV channel resets the exposure in the FUV channel with new exposure parameters. Implementation testing of the control algorithm using simulated light curves and full-frame images demonstrates a robust response to the quiescent and flaring levels expected for the stars to be monitored by the mission. The SPARCS onboard autonomous exposure control algorithm is adaptable for operation in future point source-targeting space-based and ground-based observatories geared towards the monitoring of extreme transient astrophysics phenomena.
Physical properties and real nature of massive clumps in the galaxy
Authors: Lu Zu-Jia , Pelkonen Veli-Matti , Juvela Mika , Padoan Paolo , Haugbølle Troels , Nordlund Åke 
Published: December 2021

ABSTRACT
Systematic surveys of massive clumps have been carried out to study the conditions leading to the formation of massive stars. These clumps are typically at large distances and unresolved, so their physical properties cannot be reliably derived from the observations alone. Numerical simulations are needed to interpret the observations. To this end, we generate synthetic Herschel observations using our large-scale star-formation simulation, where massive stars explode as supernovae driving the interstellar-medium turbulence. From the synthetic observations, we compile a catalogue of compact sources following the exact same procedure as for the Hi-GAL compact source catalogue. We show that the sources from the simulation have observational properties with statistical distributions consistent with the observations. By relating the compact sources from the synthetic observations to their 3D counterparts in the simulation, we find that the synthetic observations overestimate the clump masses by about an order of magnitude on average due to line-of-sight projection, and projection effects are likely to be even worse for Hi-GAL Inner Galaxy sources. We also find that a large fraction of sources classified as protostellar are likely to be starless, and propose a new method to partially discriminate between true and false protostellar sources.
Infrared analysis of Valine degradation by keV electrons. Measurements and CASINO-extended model predictions
Authors: da Costa Cíntia A P , da Silveira Enio F 
Published: December 2021

ABSTRACTDegradation of L-valine by 0.06–1.0-keV electron beams is analysed in laboratory, at 10, 150, and 300 K. Valine film thicknesses are measured by profilometry, permitting band strength determination for selected valine bands. The column density evolutions during the irradiation are measured via infrared spectroscopy and destruction cross-sections are extracted; the latter range from 1–100 × 10−16 cm2. Data show that, in general, destruction cross-sections depend not only on projectile energy and sample temperature but also on sample thickness and beam fluence. In order to understand these findings, a statistical model is proposed for describing the radiolysis of organic materials. Comparing predictions with experimental results for valine, the main trends are reproduced. The quantitative disagreement indicates that it is necessary to include sputtering in the model. A major contribution of the model is to permit to simulate, layer by layer, the sample degradation rate as a function of fluence. The model assumes that the destruction cross-section of precursor molecules is proportional to the local stopping power and uses the Monte Carlo CASINO code to determine the deposited energy distribution in the bulk. As astrophysical implications, the radiolysis of valine dissolved in H2O ice and shielded by a CO2 layer is predicted, as an attempt to analyse the degradation of realistic cosmic materials by keV electrons.
Establishing clinical remission criteria and the framework of a treat-to-target algorithm for Takayasu arteritis: Results of a Delphi exercise carried out by an expert panel of the Japan Research Committee of the Ministry of Health, Labour and Welfare for intractable vasculitis
Authors: Sugihara Takahiko , Nakaoka Yoshikazu , Uchida Haruhito A , Yoshifuji Hajime , Maejima Yasuhiro , Watanabe Yoshiko , Amiya Eisuke , Tanemoto Kazuo , Miyata Tetsuro , Umezawa Natsuka , Manabe Yusuke , Ishizaki Jun , Shirai Tsuyoshi , Nagafuchi Hiroko , Hasegawa Hitoshi , Miyamae Takako , Niiro Hiroaki , Ito Shuichi , Ishii Tomonori , Isobe Mitsuaki , Harigai Masayoshi 
Published: December 2021

ABSTRACT

Objectives
To develop a proposal for remission criteria and a framework for a treat-to-target (T2T) algorithm for Takayasu arteritis (TAK).

Methods
A study group of the large-vessel vasculitis group of the Japanese Research Committee of the Ministry of Health, Labour and Welfare for Intractable Vasculitis consists of 10 rheumatologists, 5 cardiologists, 1 nephrologist, 1 vascular surgeon, 1 cardiac surgeon, and 2 paediatric rheumatologists. A Delphi survey of remission criteria items was circulated among the study group over four reiterations. To develop the T2T algorithm, the study group conducted four face-to-face meetings and two rounds of Delphi together with three patients.

Results
Initial literature review resulted in a list of 117 candidate items for remission criteria, of which 56 items with a mean score of ≥4 (0–5) were extracted including disease activity domains and treatment/comorbidity domains. The study group provided six overarching principles for the T2T algorithm, two recommendations on treatment goals, five on evaluation of disease activity and imaging findings including positron emission tomography–computed tomography, and two on treatment intensification.

Conclusions
We developed a T2T algorithm and proposals for standardised remission criteria by means of a Delphi exercise. These will guide future evaluation of different TAK treatment regimens.
miR-144-3p aggravated cartilage injury in rheumatoid arthritis by regulating BMP2/PI3K/Akt axis
Authors: Mo Mei-Li , Jiang Jin-Mei , Long Xiao-Ping , Xie Li-Hu 
Published: December 2021

ABSTRACT

Objectives
Present study aimed to illustrate the role of miR-144-3p in rheumatoid arthritis (RA).

Methods
N1511 chondrocytes were stimulated by interleukin (IL)-1β to mimic RA injury model in vitro. Rats were subjected to injection of type II collagen to establish an in vivo RA model, and the arthritis index score was calculated. Cell viability was determined by Cell Counting Kit-8. The expression of cartilage extracellular matrix proteins (collagen II and aggrecan) and matrix metalloproteinase protein were determined by quantitative real-time polymerase chain reaction and western blots. Cell apoptosis was measured by flow cytometry. Enzyme-linked immunosorbent assay was applied to test the secretion of pro-inflammatory cytokines (IL-1β and tumour necrosis factor-α). Tissue injury and apoptosis were detected by haematoxylin–eosin staining and terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labelling assay staining. Interaction of miR-144-3p and bone morphogenetic protein 2 (BMP2) was verified by dual-luciferase assay.

Results
miR-144-3p was dramatically increased in IL-1β-induced N1511 cells. miR-144-3p depletion elevated cell viability, suppressed apoptosis, pro-inflammatory cytokine releasing, and extracellular matrix loss in IL-1β-induced N1511 cells. Moreover, miR-144-3p targeted BMP2 to modulate its expression negatively. Activation of phosphatidylinositol 3-kinase (PI3K)/Akt signalling compromised inhibition of BMP2 induced aggravated N1511 cell injury with IL-1β stimulation. Inhibition of miR-144-3p alleviated cartilage injury and inflammatory in RA rats.

Conclusion
Collectively, miR-144-3p could aggravate chondrocyte injury inflammatory response in RA via BMP2/PI3K/Akt axis.
Performance of recent PRINTO criteria versus current ILAR criteria for systemic juvenile idiopathic arthritis: A single-centre experience
Authors: Koker Oya , Demirkan Fatma Gul , Cakmak Figen , Aktay Ayaz Nuray 
Published: December 2021

ABSTRACT

Objectives
The purpose of this study is to evaluate the performances of recently proposed Pediatric Rheumatology International Trials Organization criteria versus current International League of Associations for Rheumatology criteria for systemic juvenile idiopathic arthritis (sJIA).

Methods
The study was performed at the Department of Pediatric Rheumatology in Istanbul Faculty of Medicine with a retrospective design, covering the date range 2010–2021. Patients diagnosed with sJIA, Kawasaki disease and common autoinflammatory diseases were included. Both the International League of Associations for Rheumatology and Pediatric Rheumatology International Trials Organization classification criteria were applied to each patient and cross-checked with expert rheumatologist diagnosis.

Results
Eighty-two patients with sJIA were compared against 189 (74 Kawasaki disease, 83 familial Mediterranean fever, 16 mevalonate kinase deficiency, 10 cryopyrin-associated periodic syndromes, and 6 tumour necrosis factor receptor-associated periodic syndrome) patients. The Pediatric Rheumatology International Trials Organization criteria demonstrated higher sensitivity (62.2% vs 80.5%, P =.003) but comparable specificity (90.5% vs 91%) as regards the International League of Associations for Rheumatology criteria.

Conclusions
The revised criteria appear to enhance the ability to provide early recognition and pertinent classification of sJIA. No superiority was observed in segregating sJIA from common autoinflammatory diseases and Kawasaki disease, namely in terms of specificity.
A case of giant cell arteritis lacking typical symptoms presenting with recurrent cerebellar infarctions: A case report and case-based review
Authors: Hiyama Ryuichiro , Oiwa Hiroshi , Kanou Yukari , Nishibe Shiho , Kono Tomoyuki , Nomura Eiichi 
Published: December 2021

ABSTRACT
Giant cell arteritis (GCA) occasionally presents with ischaemic stroke. Generally, symptoms related to GCA or elevated levels of inflammation markers would be a clue for the diagnosis of GCA. However, we encountered a rare case of GCA that presented with recurrent cerebellar infarctions without symptoms related to GCA (headache, fever, or jaw claudication). Furthermore, C-reactive protein levels, measured at the time of two of the stroke attacks, were within the normal range. On physical examination, the temporal arteries were prominent and weakly pulsatile. Temporal artery ultrasonography showed halo signs, and temporal artery biopsy revealed GCA. To our knowledge, this is the first case of GCA presenting with recurrent ischaemic stroke lacking GCA features but diagnosed before death. Considering this case-based review, we suggest that GCA may have been missed in elderly patients with ischaemic stroke, especially in those with posterior circulation infarction. Therefore, physical examination of the temporal arteries, temporal artery ultrasonography, and vessel wall magnetic resonance imaging may be useful in those patients.
Acute encephalitis in primary Sjögren’s syndrome: A case report and literature review
Authors: Higashida-Konishi Misako , Akiyama Mitsuhiro , Shimada Tatsuya , Hama Satoshi , Takei Hiroshi , Izumi Keisuke , Oshima Hisaji , Okano Yutaka 
Published: December 2021

ABSTRACT
Acute encephalitis is an extremely rare condition in primary Sjogren’s syndrome (pSS), and its characteristics and prognosis remain unclear. Here, we report the case of pSS presented with acute encephalitis. She was admitted to our hospital for acute disturbance of consciousness. Acute encephalitis was diagnosed based on the results of the cerebrospinal fluid test (the increase of leucocyte counts, proteins, and interleukin-6 levels), magnetic resonance imaging, and single-photon emission computed tomography with 99mTc. The infectious aetiologies and underlying malignancies were excluded. Serum anti-Sjogren’s syndrome-related antigen A autoantibody was positive with extremely high titre. The biopsy specimen of her labial salivary gland revealed a focal lymphocytic sialadenitis with a score of grade 4 in the Greenspan grade. She also developed diffuse alveolar haemorrhage during the clinical course. She was diagnosed with pSS complicated with acute encephalitis followed by diffuse alveolar haemorrhage and successfully treated with pulse steroids, high dose of prednisolone and intravenous cyclophosphamide. Our present case and literature review suggest that acute encephalitis associated with pSS can be treatable with the immunosuppressive therapy, and thus early recognition and treatment initiation are important for this life-threatening condition. Thus, pSS should be included in the differential diagnosis of unexplained encephalitis. Notably, our case characteristically showed diffuse alveolar haemorrhage, adding new insights into the pathogenesis of acute encephalitis associated with pSS that capillaritis might be the underlying cause of this condition.
Canonical and novel non-canonical activities of the Holliday junction resolvase Yen1
Authors: Carreira Raquel , Aguado F Javier , Hurtado-Nieves Vanesa , Blanco Miguel G 
Published: December 2021

Abstract
Yen1 and GEN1 are members of the Rad2/XPG family of nucleases that were identified as the first canonical nuclear Holliday junction (HJ) resolvases in budding yeast and humans due to their ability to introduce two symmetric, coordinated incisions on opposite strands of the HJ, yielding nicked DNA products that could be readily ligated. While GEN1 has been extensively characterized in vitro, much less is known about the biochemistry of Yen1. Here, we have performed the first in-depth characterization of purified Yen1. We confirmed that Yen1 resembles GEN1 in many aspects, including range of substrates targeted, position of most incisions they produce or the increase in the first incision rate by assembly of a dimer on a HJ, despite minor differences. However, we demonstrate that Yen1 is endowed with additional nuclease activities, like a nick-specific 5′-3′ exonuclease or HJ arm-chopping that could apparently blur its classification as a canonical HJ resolvase. Despite this, we show that Yen1 fulfils the requirements of a canonical HJ resolvase and hypothesize that its wider array of nuclease activities might contribute to its function in the removal of persistent recombination or replication intermediates.
PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments
Authors: Smith Jason P , Corces M Ryan , Xu Jin , Reuter Vincent P , Chang Howard Y , Sheffield Nathan C 
Published: December 2021

Abstract
As chromatin accessibility data from ATAC-seq experiments continues to expand, there is continuing need for standardized analysis pipelines. Here, we present PEPATAC, an ATAC-seq pipeline that is easily applied to ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. PEPATAC leverages unique features of ATAC-seq data to optimize for speed and accuracy, and it provides several unique analytical approaches. Output includes convenient quality control plots, summary statistics, and a variety of generally useful data formats to set the groundwork for subsequent project-specific data analysis. Downstream analysis is simplified by a standard definition format, modularity of components, and metadata APIs in R and Python. It is restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also demonstrate the advantage of aligning to the mitochondrial genome serially, which improves the accuracy of alignment statistics and quality control metrics. PEPATAC is a robust and portable first step for any ATAC-seq project. BSD2-licensed code and documentation are available at https://pepatac.databio.org.
ChiTaH: a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data
Authors: Detroja Rajesh , Gorohovski Alessandro , Giwa Olawumi , Baum Gideon , Frenkel-Morgenstern Milana 
Published: December 2021

Abstract
Fusion genes or chimeras typically comprise sequences from two different genes. The chimeric RNAs of such joined sequences often serve as cancer drivers. Identifying such driver fusions in a given cancer or complex disease is important for diagnosis and treatment. The advent of next-generation sequencing technologies, such as DNA-Seq or RNA-Seq, together with the development of suitable computational tools, has made the global identification of chimeras in tumors possible. However, the testing of over 20 computational methods showed these to be limited in terms of chimera prediction sensitivity, specificity, and accurate quantification of junction reads. These shortcomings motivated us to develop the first ‘reference-based’ approach termed ChiTaH (Chimeric Transcripts from High–throughput sequencing data). ChiTaH uses 43,466 non–redundant known human chimeras as a reference database to map sequencing reads and to accurately identify chimeric reads. We benchmarked ChiTaH and four other methods to identify human chimeras, leveraging both simulated and real sequencing datasets. ChiTaH was found to be the most accurate and fastest method for identifying known human chimeras from simulated and sequencing datasets. Moreover, especially ChiTaH uncovered heterogeneity of the BCR-ABL1 chimera in both bulk and single-cells of the K-562 cell line, which was confirmed experimentally.