bluuebunny/crossref_metadata_2025_split huggingface dataset:
The nature of 500 micron risers – II. Multiplicities and environments of sub-mm faint dusty star-forming galaxies
Authors: Cairns J , Clements D L , Greenslade J , Petitpas G , Cheng T , Ding Y , Parmar A , Pérez-Fournon I , Riechers D 
Published: November 2022

ABSTRACT
We present Submillimeter Common User Bolometer Array 2 (SCUBA-2) and Submillimeter Array (SMA) follow-up observations of four candidate high-redshift dusty star-forming galaxies, selected as sources with rising spectral energy distributions in the 250, 350, and 500 μm Herschel SPIRE bands. Previous SMA observations showed no counterparts to these sources, but in our deeper sub-mm observations we detect counterparts to all four 500 μm risers, with three resolving into multiple systems. For these three multiple systems, the SMA 345 GHz (≈870 μm) observations recover $123 \pm 73{{\ \rm per\ cent}}$, $60 \pm 15{{\ \rm per\ cent}}$, and $19 \pm 4{{\ \rm per\ cent}}$ of the integrated 850 μm flux density from SCUBA-2, indicating that there may be additional sources below our SMA detection limit making up a dense, protocluster core. The fourth 500 μm riser was observed at a lower frequency and so we cannot make a similar comparison. We estimate photometric redshifts based on FIR/sub-mm colours, finding that three fourths likely lie at z ≥ 2. This fits with the interpretation that the 500 μm riser selection criterion selects both intrinsically red, individual galaxies at z &gt; 4, and multiple systems at more moderate redshifts, artificially reddened by the effects of blending. We use the SCUBA-2 850 μm maps to investigate the environments of these 500 μm risers. By constructing cumulative number counts and estimating photometric redshifts for surrounding SCUBA-2 detections, we find that one of our 500 μm risers could plausibly reside in a z ≥ 2 protocluster. We infer that bright 500 μm risers with faint 850 μm flux densities are typically multiple systems at z ≥ 2 that may reside in overdensities of bright sub-mm galaxies.
The development and use of metal-based probes for X-ray fluorescence microscopy
Authors: Victor-Lovelace Tiffany W , Miller Lisa M 
Published: November 2022

Abstract
X-ray fluorescence microscopy (XFM) has become a widely used technique for imaging the concentration and distribution of metal ions in cells and tissues. Recent advances in synchrotron sources, optics, and detectors have improved the spatial resolution of the technique to &lt;10 nm with attogram detection sensitivity. However, to make XFM most beneficial for bioimaging—especially at the nanoscale—the metal ion distribution must be visualized within the subcellular context of the cell. Over the years, a number of approaches have been taken to develop X-ray-sensitive tags that permit the visualization of specific organelles or proteins using XFM. In this review, we examine the types of X-ray fluorophore used, including nanomaterials and metal ions, and the approaches used to incorporate the metal into their target binding site via antibodies, genetically encoded metal-binding peptides, affinity labeling, or cell-specific peptides. We evaluate their advantages and disadvantages, review the scientific findings, and discuss the needs for future development.
GENCODE: reference annotation for the human and mouse genomes in 2023
Authors: Frankish Adam , Carbonell-Sala Sílvia , Diekhans Mark , Jungreis Irwin , Loveland Jane E , Mudge Jonathan M , Sisu Cristina , Wright James C , Arnan Carme , Barnes If , Banerjee Abhimanyu , Bennett Ruth , Berry Andrew , Bignell Alexandra , Boix Carles , Calvet Ferriol , Cerdán-Vélez Daniel , Cunningham Fiona , Davidson Claire , Donaldson Sarah , Dursun Cagatay , Fatima Reham , Giorgetti Stefano , Giron Carlos Garcıa , Gonzalez Jose Manuel , Hardy Matthew , Harrison Peter W , Hourlier Thibaut , Hollis Zoe , Hunt Toby , James Benjamin , Jiang Yunzhe , Johnson Rory , Kay Mike , Lagarde Julien , Martin Fergal J , Gómez Laura Martínez , Nair Surag , Ni Pengyu , Pozo Fernando , Ramalingam Vivek , Ruffier Magali , Schmitt Bianca M , Schreiber Jacob M , Steed Emily , Suner Marie-Marthe , Sumathipala Dulika , Sycheva Irina , Uszczynska-Ratajczak Barbara , Wass Elizabeth , Yang Yucheng T , Yates Andrew , Zafrulla Zahoor , Choudhary Jyoti S , Gerstein Mark , Guigo Roderic , Hubbard Tim J P , Kellis Manolis , Kundaje Anshul , Paten Benedict , Tress Michael L , Flicek Paul 
Published: November 2022

Abstract
GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
Nicotine Enhances Intravenous Self-administration of Cannabinoids in Adult Rats
Authors: Stringfield Sierra J , Sanders Bryson E , Suppo Jude A , Sved Alan F , Torregrossa Mary M 
Published: November 2022

AbstractIntroductionNicotine and cannabis are commonly used together, yet few studies have investigated the effects of concurrent administration. Nicotine exhibits reinforcement enhancing effects by promoting the reinforcing properties of stimuli including other drugs. As many studies of this effect used non-contingent nicotine, we implemented a dual-self-administration model where rats have simultaneous access to two drugs and choose which to self-administer throughout a session. Here, we investigated the effect of self-administered or non-contingently delivered nicotine on cannabinoid self-administration.MethodsAdult male rats were allowed to self-administer the synthetic cannabinoid WIN 55,212-2 (WIN) intravenously, with or without subcutaneous nicotine injections before each session. A separate group of animals were allowed to self-administer WIN, nicotine, or saline using a dual-catheter procedure, where each solution was infused independently and associated with a separate operant response. A third group of male and female rats were allowed to self-administer delta-9-tetrahydrocannabinol (THC) with or without pre-session injections of nicotine.ResultsNicotine injections increased self-administration of WIN and THC. During dual self-administration, nicotine availability increased saline and WIN infusions but nicotine intake was not changed by WIN or saline availability. Rats preferred nicotine over saline, but preferred nicotine and WIN equally when both were available. The effect of nicotine on cannabinoid self-administration was acute and reversible when nicotine was no longer present.ConclusionsThese results expand our understanding of the ability of nicotine to enhance reinforcement of other drugs and suggest that co-use of nicotine and cannabinoids promotes cannabinoid use beyond what would be taken alone.ImplicationsThis study utilizes a dual intravenous self-administration model to investigate the ability of nicotine to enhance cannabinoid intake. Our results demonstrate that the reinforcement enhancing properties of nicotine on drug use extend to include cannabinoids, but that this effect occurs specifically when nicotine is administered alongside the cannabinoid. Interestingly, cannabinoid use did not promote nicotine intake, suggesting this mechanism of reinforcement is specific to nicotine.
Epstein-Barr Virus Glycoprotein Antibody Titers and Risk of Nasopharyngeal Carcinoma
Authors: Coghill Anna E , McGuire Andrew , Sinha Sweta , Homad Leah , Sinha Irika , Sholukh Anton , Koh Woon-Puay , Yuan Jian Min 
Published: November 2022

Abstract
We evaluated antibody against Epstein-Barr virus glycoproteins (gp350, gH/gL, gB, gp42) in 97 nasopharyngeal carcinoma (NPC) cases and 97 cancer-free controls. Each unit increase in log-transformed antibody against gp350 and gH/gL was associated with 2.27 (95% confidence interval [CI], 1.20–4.29) and 2.18 (95% CI, 1.22–3.90) higher odds of NPC, respectively. This association was more apparent for NPC diagnosed within 5 years of antibody measurement.
PHOSPHATE RESPONSE 1 family members act distinctly to regulate transcriptional responses to phosphate starvation
Authors: Wang Zhen , Zheng Zai , Zhu Yumin , Kong Shuyao , Liu Dong 
Published: November 2022

Abstract
To sustain growth when facing phosphate (Pi) starvation, plants trigger an array of adaptive responses that are largely controlled at transcriptional levels. In Arabidopsis (Arabidopsis thaliana), the four transcription factors of the PHOSPHATE RESPONSE 1 (PHR1) family, PHR1 and its homologs PHR1-like 1 (PHL1), PHL2, and PHL3 form the central regulatory system that controls the expression of Pi starvation-responsive (PSR) genes. However, how each of these four proteins function in regulating the transcription of PSR genes remains largely unknown. In this work, we performed comparative phenotypic and transcriptomic analyses using Arabidopsis mutants with various combinations of mutations in these four genes. The results showed that PHR1/PHL1 and PHL2/PHL3 do not physically interact with each other and function as two distinct modules in regulating plant development and transcriptional responses to Pi starvation. In the PHR1/PHL1 module, PHR1 plays a dominant role, whereas, in the PHL2/PHL3 module, PHL2 and PHL3 contribute similarly to the regulation of PSR gene transcription. By analyzing their common and specific targets, we showed that these PHR proteins could function as both positive and negative regulators of PSR gene expression depending on their targets. Some interactions between PHR1 and PHL2/PHL3 in regulating PSR gene expression were also observed. In addition, we identified a large set of defense-related genes whose expression is not affected in wild-type plants but is altered in the mutant plants under Pi starvation. These results increase our understanding of the molecular mechanism underlying plant transcriptional responses to Pi starvation.
Associations between levels of Internet Gaming Disorder symptoms and striatal morphology–replication and associations with social anxiety
Authors: Klugah-Brown Benjamin , Zhou Xinqi , Wang Lan , Gan Xianyang , Zhang Ran , Liu Xiqin , Song Xinwei , Zhao Weihua , Biswal Bharat B , Yu Fangwen , Montag Christian , Becker Benjamin 
Published: November 2022

AbstractBackgroundBrain structural alterations of the striatum have been frequently observed in internet gaming disorder (IGD); however, the replicability of the results and the associations with social-affective dysregulations such as social anxiety remain to be determined.MethodsThe present study combined a dimensional neuroimaging approach with both voxel-wise and data-driven multivariate approaches to (i) replicate our previous results on a negative association between IGD symptom load (assessed by the Internet Gaming Disorder Scale-Short Form) and striatal volume, (ii) extend these findings to female individuals, and (iii) employ multivariate and mediation models to determine common brain structural representations of IGD and social anxiety (assessed by the Liebowitz Social Anxiety Scale).ResultsIn line with the original study, the voxel-wise analyses revealed a negative association between IGD and volumes of the bilateral caudate. Going beyond the earlier study investigating only male participants, the present study demonstrates that the association in the right caudate was comparable in both the male and the female subsamples. Further examination using the multivariate approach revealed regionally different associations between IGD and social anxiety with striatal density representations in the dorsal striatum (caudate) and ventral striatum (nucleus accumbens). Higher levels of IGD were associated with higher social anxiety and the association was critically mediated by the multivariate neurostructural density variations of the striatum.ConclusionsAltered striatal volumes may represent a replicable and generalizable marker of IGD symptoms. However, exploratory multivariate analyses revealed more complex and regional specific associations between striatal density and IGD as well as social anxiety symptoms. Variations in both tendencies may share common structural brain representations, which mediate the association between increased IGD and social anxiety.
Patient safety practices in European anaesthesiology
Authors: McCreedy Aimee , Wacker Johannes , Ffrench-O’Carroll Robert , Berthelsen Kasper Gymoese , Kremeňova Tatičová Zuzana , Smith Andrew F. 
Published: November 2022

BACKGROUND
Patient safety is a key concern of anaesthesiology practice. However, good practices are often not widely shared between departments and hospitals, whether within or between countries.

OBJECTIVE
We aimed to collect and analyse safety practices and tips from anaesthesiology departments around Europe in order to facilitate successful transfer of safety knowledge.

DESIGN
Review of previously collected safety practices; allocation of numerical scores in order to rank them on 0–5 scales in terms of anticipated impact, and speed, cost, and ease of implementation; free text comment on any possible difficulties or unintended harms which might arise from adopting any of the collected practices.

SETTING
Collaborative remote working of expert group.

PARTICIPANTS
Nineteen experts in patient safety in anaesthesiology from nine European countries.

MAIN OUTCOME MEASURES
Rankings of safety practices for anticipated practice impact, cost, speed, and ease of implementation.

RESULTS
We collected 117 practices. The highest-ranked items for potential beneficial impact were: standardising the layout of drug trolleys (4.82); involving all staff in new safety initiatives in the operating theatre (4.73); ensuring patients’ medical records are available at the time of surgery (4.71); running regular simulation training sessions in departments of anaesthesia (4.67); and creating a difficult airway management trolley (4.65). A major theme to emerge from the qualitative analysis of the experts’ free text comments was the risk that practices aimed at enhancing patient safety might not achieve the effect intended, as introducing new safety activities can cause more mistakes during the implementation phase.

CONCLUSION
Many useful practices to promote patient safety were identified, but as some practices appear to be context-dependent, we recommend that a proper, prospective risk assessment is carried out before they are introduced in a new setting. The full list of items is available online as Supplementary Digital Content, http://links.lww.com/EJA/A785.

TRIAL REGISTRATION
Not applicable.
Combined Therapeutic Penetrating Keratoplasty and Pars Plana Vitrectomy for the Treatment of Infectious Keratitis Endophthalmitis: Mexican Endophthalmitis Study Group Protocol 4
Authors: Velez-Montoya Raul , Rivera-Cortes Mariana A. , Ledesma-Gil Gerardo , Carranza-Casas Mario , Martinez Jaime D. , Levine Harry , Yanuzzi Nicolas A. , Amescua Guillermo , Ahmed Ishrat , Beatson Bradley , Akpek Esen , Arevalo J. Fernando , Fromow-Guerra Jans ,   for the Mexican Endophthalmitis Study Group (Mex-ESG)
Published: November 2022

Purpose:
The purpose of this study was to assess the role of combined surgical treatment of therapeutic penetrating keratoplasty and pars plana vitrectomy in the anatomical and functional outcome of infectious keratitis endophthalmitis.

Methods:
This study reviewed the medical records of 4 participating centers in the United States and Mexico. This study included patients with a clinical diagnosis of infectious keratitis endophthalmitis who had been treated with an early therapeutic penetrating keratoplasty and pars plana vitrectomy as the main treatment for endophthalmitis. From each medical record, the study retrieved demographic data, relevant medical and drug history, baseline clinical manifestation of endophthalmitis, best-corrected visual acuity, and the need for enucleation/evisceration for the control of the infection or any other reason through the follow-up.

Results:
The study included 48 patients (50.15 ± 20.6 years). The mean follow-up time was 13 ± 0.5 months. The mean best-corrected visual acuity at baseline was 2.1 ± 0.25 logarithm of the minimum angle of resolution. At month 12 was 2.09 ± 0.61 logarithm of the minimum angle of resolution (P = 0.9). The overall prevalence of enucleation/evisceration was 8.3% (95% confidence interval: 2.32%–19.98%). The prevalence of a vision of no-light perception was 20.8% (95% confidence interval: 2.32%–19.98%).

Conclusions:
Combined surgery for severe cases of infectious keratitis endophthalmitis eradicates the infection in most cases, while significantly improving the overall outcomes.
Management of acute severe hypertension in youth: from the philosophical to the practical
Authors: Giammattei Victoria C. , Weaver Donald J. , South Andrew M. 
Published: November 2022

Purpose of review
Acute severe hypertension remains an uncommon but important source of morbidity and mortality in youth. However, there has been very little progress made in our understanding of how to best manage youth with acute severe hypertension to improve patient outcomes.

Recent findings
Our understanding of what is acute severe hypertension is undergoing a philosophical change. Management of patients with acute severe hypertension is evolving towards more of a risk and outcomes-based approach.

Summary
We should be intentional when we consider whether a patient has acute severe hypertension and if they are truly at an increased risk for life-threatening target organ injury. We should consider their specific risk factors to best interpret the risks and benefits of how best to treat a patient with acute severe hypertension, rather than relying on traditional approaches and conventional wisdom. We should always ask ‘why’ when we are pursuing a given management course. Future studies should clearly define the research questions they are investigating to best advance the field to ultimately improve patient outcomes.
Epigenome-wide association study of serum folate in maternal peripheral blood leukocytes
Authors: Fragoso-Bargas N. , Page C.M. , Joubert B.R. , London S.J. , Lee-Ødegård S. , Opsahl J.O. , Sletner L. , Jenum A.K. , Qvigstad E. , Prasad R.B. , Moen G.-H. , Birkeland K.I. , Sommer C. 
Published: November 2022

AbstractAimTo perform an epigenome-wide association study (EWAS) of serum folate in maternal blood.MethodsWe performed cross-ancestry (Europeans=302, South Asians=161) and ancestry-specific EWAS in the EPIPREG cohort, followed by methyl quantitative trait loci (mQTL) analysis and association with cardiometabolic phenotypes. We attempted replication using folate intake estimated from a food frequency questionnaire and maternal blood methylation data from MoBa, and in a previous published EWAS of maternal serum folate in cord blood.Resultscg19888088 (cross-ancestry) inEBF3, cg01952260 (Europeans), and cg07077240 (South Asians) inHERC3were associated with serum folate. cg19888088 and cg01952260 were associated with diastolic blood pressure. cg07077240 was associated with variants inCASC15. The findings were not replicated in the independent samples.ConclusionSerum folate was associated with methylation at three CpG sites.
Assessment of Attitude and Hesitancy Towards Covid-19 Vaccine among Hepatitis B and C Patients in Pakistan
Authors: Shafiq Farheen , Hassan Mahreen ul , Butt Sadia , Sidique Sadia , Akbar Nazia , Azra  , Rehman Irshad 
Published: November 2022

ABSTRACTOBJECTIVEThe research aimed to evaluate the attitude and perceptions towards the covid-19 vaccine among Hepatitis B and C patients in Peshawar, Khyber Pakhtunkhwa, Muzaffarabad, Azad Kashmir, Pakistan.METHODSA survey-based study was adopted to evaluate the attitude of Hepatitis B and C patients towards immunization against covid-19 in Peshawar (KPK) and Muzaffarabad (AJK) cities of Pakistan. The study continued from January 2020 to February 2021. Participants were also assessed for their perception towards covid-19 vaccination.RESULTSA total of 839 (33.6%) individuals participated in the study. About 52 % of Hepatitis B patients were immunized against Covid-19, whereas the number of Hepatitis C patients was recorded at around 48%. About 53.7 % of participants refused to get the vaccine without any reason. About 63.2% of patients showed concern about the insufficient data available on the vaccine safety and efficacy published by the Public Health Department. Individuals with higher education were observed to be more open towards vaccination then those without a formal education. More than half of the participants (61.5 %) were concerned about the interference of the vaccine with their hepatitis treatment whereas 54.7 % patients refused vaccine because of a poor liver condition.CONCLUSIONSThe data indicated that limited data availability regarding the vaccine efficacy in viral hepatitis patients and negative attitudes of people toward covid-19 vaccination is the main cause of Covid-19 vaccination refusal among hepatitis B and C patients.DESCRIPTORSHepatitis B, Hepatitis C, covid-19, immunization, vaccine refusal, Pakistan.
A Multimodal Atlas of Tumor Metabolism Reveals the Architecture of Gene-Metabolite Co-regulation
Authors: Benedetti Elisa , Liu Eric Minwei , Tang Cerise , Kuo Fengshen , Buyukozkan Mustafa , Park Tricia , Park Jinsung , Correa Fabian , Hakimi A Ari , Intlekofer Andrew , Krumsiek Jan , Reznik Ed 
Published: November 2022

AbstractTumor metabolism is controlled by coordinated changes in metabolite abundance and gene expression, but simultaneous quantification of metabolites and transcripts in primary tissue is rare. To overcome this limitation and study gene-metabolite coregulation in cancer, we assembled the Cancer Atlas of Metabolic Profiles (cAMP) of metabolomic and transcriptomic data from 988 tumor/normal specimens spanning 11 cancer types. Meta-analysis of the cAMP revealed two classes of Gene-Metabolite Interactions (GMIs) that transcended cancer types. The first corresponded to a small number of gene-metabolite pairs engaged in direct enzyme-substrate interactions, identifying putative metabolite-pool-size-controlling genes. A second class of GMIs represented a small number of hub metabolites, including quinolinate and NAD+, which correlated to many genes specifically expressed on immune cell populations. These results provide evidence that gene-metabolite coregulation in human tissue arises, in part, from both mechanistic interactions between genes/metabolites, and from metabolic remodeling in specific immune microenvironments.