bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plassembler: an automated bacterial plasmid assembly tool
Authors: Bouras George , Sheppard Anna E , Mallawaarachchi Vijini , Vreugde Sarah 
Published: June 2023

Abstract

Summary
With recent advances in sequencing technologies, it is now possible to obtain near-perfect complete bacterial chromosome assemblies cheaply and efficiently by combining a long-read-first assembly approach with short-read polishing. However, existing methods for assembling bacterial plasmids from long-read-first assemblies often misassemble or even miss bacterial plasmids entirely and accordingly require manual curation. Plassembler was developed to provide a tool that automatically assembles and outputs bacterial plasmids using a hybrid assembly approach. It achieves increased accuracy and computational efficiency compared to the existing gold standard tool Unicycler by removing chromosomal reads from the input read sets using a mapping approach.

Availability and implementation
Plassembler is implemented in Python and is installable as a bioconda package using ‘conda install -c bioconda plassembler’. The source code is available on GitHub at https://github.com/gbouras13/plassembler. The full benchmarking pipeline can be found at https://github.com/gbouras13/plassembler_simulation_benchmarking, while the benchmarking input FASTQ and output files can be found at https://doi.org/10.5281/zenodo.7996690.
Accelerating the alignment processing speed of the comprehensive end-to-end whole-genome bisulfite sequencing pipeline, wg-blimp
Authors: Lehle Jake D , McCarrey John R 
Published: June 2023

Abstract
Analyzing whole-genome bisulfite and related sequencing datasets is a time-intensive process due to the complexity and size of the input raw sequencing files and lengthy read alignment step requiring correction for conversion of all unmethylated Cs to Ts genome-wide. The objective of this study was to modify the read alignment algorithm associated with the whole-genome bisulfite sequencing methylation analysis pipeline (wg-blimp) to shorten the time required to complete this phase while retaining overall read alignment accuracy. Here, we report an update to the recently published pipeline wg-blimp achieved by replacing the use of the bwa-meth aligner with the faster gemBS aligner. This improvement to the wg-blimp pipeline has led to a more than ×7 acceleration in the processing speed of samples when scaled to larger publicly available FASTQ datasets containing 80–160 million reads while maintaining nearly identical accuracy of properly mapped reads when compared with data from the previous pipeline. The modifications to the wg-blimp pipeline reported here merge the speed and accuracy of the gemBS aligner with the comprehensive analysis and data visualization assets of the wg-blimp pipeline to provide a significantly accelerated workflow that can produce high-quality data much more rapidly without compromising read accuracy at the expense of increasing RAM requirements up to 48 GB.
Relational Police Work: How Police Officers Work With, On and Through ‘Personal Relationships’ in a Danish Gang Exit Programme
Authors: Johansen Mette-Louise E 
Published: June 2023

AbstractThis article examines how police-assisted gang desistance in Denmark is run on the backdrop of a particular kind of ‘relational work’ that focuses on relationships as the basis for change. The analysis is based on ethnographic fieldwork and interviews conducted in 2020 with police officers, social workers and gang defectors attached to the city of Aarhus Exit Unit, part of Denmark’s national gang exit programme. The Exit Unit’s relational work consisted of creating close, personal relationships with defectors, which could serve as a vehicle for interventions into the defectors’ relationships with gangs, family, friends and neighbourhoods. This relational work was highly ambiguous; it entailed dual practices of correctional control and help to reposition defectors in-between criminal and non-criminal social worlds.
Coproduction with Service Users in Adult Social Work: A Study of Service Users’ and Social Workers’ Experiences in Northern Ireland
Authors: Burns Patricia , McGinn Tony , Fitzsimons Lelia 
Published: June 2023

Abstract
Involving service users, in the delivery of health and social care, is a focal point in social policy discourse. Coproduction has become synonymous with anti-oppressive practice and service user empowerment. This article reports on a qualitative study carried out in Northern Ireland which explored service user involvement in adult social care practice and policy development. Semi-structured interviews were completed with service users (n = 6) and social workers (n = 7); thematic analysis was applied to the resultant data. The study was coproduced with service users who informed the research design and were actively involved throughout each phase of the study. Findings suggest that service users are motivated to participate in coproduction and can feel valued in these roles, but meaningful coproduction is a challenge in the current practice environment. Close working relationships, with clear and consistent communication are difficult to maintain amid the current trend of bureaucratisation in our profession. Findings point towards the need for a service-user/social worker alliance which can challenge problematic organisational cultures. Remuneration for service users, engaged in coproduction, is encouraged, alongside organisational recognition of the time and resource necessary for effective coproduction. A procedural and ethical framework for coproduction practices would also be timely.
Coexistence of psoriasis and cutaneous T-cell lymphoma
Authors: Scott Joseph , Lai Chester , Coltart George , Bates Andrew , Bennett Luke , Sommerlad Matthew , Foria Vipul , Healy Eugene 
Published: June 2023

Abstract
It has been reported that individuals with psoriasis are at an increased risk of developing cutaneous T-cell lymphoma (CTCL). However, the increased risk of lymphoma in these patients has been questioned because CTCL in its early stages may be incorrectly labelled as psoriasis, thus introducing potential for misclassification bias. We retrospectively reviewed patients with a confirmed diagnosis of CTCL seen in a tertiary cutaneous lymphoma clinic (n = 115) over a 5-year period and found that 6 (5.2%) patients had clinical evidence of coexisting psoriasis. This demonstrates that there is a small cohort of individuals who develop both psoriasis and CTCL.
Age differences in neural distinctiveness during memory encoding, retrieval, and reinstatement
Authors: Pauley Claire , Kobelt Malte , Werkle-Bergner Markus , Sander Myriam C 
Published: June 2023

Abstract
Robust evidence points to mnemonic deficits in older adults related to dedifferentiated, i.e. less distinct, neural responses during memory encoding. However, less is known about retrieval-related dedifferentiation and its role in age-related memory decline. In this study, younger and older adults were scanned both while incidentally learning face and house stimuli and while completing a surprise recognition memory test. Using pattern similarity searchlight analyses, we looked for indicators of neural dedifferentiation during encoding, retrieval, and encoding–retrieval reinstatement. Our findings revealed age-related reductions in neural distinctiveness during all memory phases in visual processing regions. Interindividual differences in retrieval- and reinstatement-related distinctiveness were strongly associated with distinctiveness during memory encoding. Both item- and category-level distinctiveness predicted trial-wise mnemonic outcomes. We further demonstrated that the degree of neural distinctiveness during encoding tracked interindividual variability in memory performance better than both retrieval- and reinstatement-related distinctiveness. All in all, we contribute to meager existing evidence for age-related neural dedifferentiation during memory retrieval. We show that neural distinctiveness during retrieval is likely tied to recapitulation of encoding-related perceptual and mnemonic processes.
Effects of turbidity, temperature and predation cue on the stress response of juvenile delta smelt
Authors: Pasparakis Christina , Lohroff Toni , Biefel Felix , Cocherell Dennis E , Carson Evan W , Hung Tien-Chieh , Connon Richard E , Fangue Nann A , Todgham Anne E 
Published: June 2023

Abstract
The San Francisco Estuary (SFE) is one of the most degraded ecosystems in the United States, and organisms that inhabit it are exposed to a suite of environmental stressors. The delta smelt (Hypomesus transpacificus), a small semi-anadromous fish endemic to the SFE and considered an indicator species, is close to extinction in the wild. The goal of this study was to investigate how environmental alterations to the SFE, such as reductions in turbidities, higher temperatures and increased prevalence of invasive predators affect the physiology and stress response of juvenile delta smelt. Juvenile delta smelt were exposed to two temperatures (17 and 21°C) and two turbidities (1–2 and 10–11 NTU) for 2 weeks. After the first week of exposure, delta smelt were exposed to a largemouth bass (Micropterus salmoides) predator cue at the same time every day for 7 days. Fish were measured and sampled on the first (acute) and final (chronic) day of exposures to predator cues and later analyzed for whole-body cortisol, glucose, lactate, and protein. Length and mass measurements were used to calculate condition factor of fish in each treatment. Turbidity had the greatest effect on juvenile delta smelt and resulted in reduced cortisol, increased glucose and lactate, and greater condition factor. Elevated temperatures reduced available energy in delta smelt, indicated by lower glucose and total protein, whereas predator cue exposure had negligible effects on their stress response. This is the first study to show reduced cortisol in juvenile delta smelt held in turbid conditions and adds to the growing data that suggest this species performs best in moderate temperatures and turbidities. Multistressor experiments are necessary to understand the capacity of delta smelt to respond to the multivariate and dynamic changes in their natural environment, and results from this study should be considered for management-based conservation efforts.
Catecholamine-induced Takotsubo syndrome: a case series
Authors: Campana Nicola , Gioi Alessandra , Marchetti Maria Francesca , Giusti Martina , Angius Simone , Caggiari Ludovica , Biddau Mattia , Montisci Roberta 
Published: June 2023

Abstract

Background
Catecholamine-induced Takotsubo Syndrome (cat-TS) is a type of secondary Takotsubo syndrome, characterized by rapid onset of symptoms, high rate of complications during the acute phase, good short-term prognosis, and frequent apical sparing at echocardiogram. We present two clinical cases of cat-TS treated in our department.

Case summary
Case one: 78-year-old man, admitted to Ear Nose and Throat Unit for surgical removal of oral squamous cellular carcinoma. During surgery, the occurrence of hypotensive episode was treated with catecholamines. After surgery, the occurrence of atrial fibrillation was followed by evidence of phasic increase of troponin levels and akinesia of midventricular segments. Angiography showed the absence of significant coronary stenoses, and during hospital stay, we observed rapid recovery of wall motion abnormalities. Case two: 64-year-old woman, admitted for hysteropexy surgery, during which cardiac arrest occurred, treated with epinephrine i.v.1 mg and DC shock. Two hours after resuscitation, the patient developed pulmonary oedema, troponin levels increased progressively, and the echocardiogram demonstrated hypokinesia in all midventricular segments with apical sparing. Afterwards, an urgent angiography highlighted normal coronary anatomy. Cardiac magnetic resonance imaging (MRI) revealed oedema corresponding to hypokinetic areas. On the seventh day, echocardiogram showed a complete remission of wall motion abnormalities.

Discussion
These cases warn the physicians about the importance of routinely screening myocardial impairment through clinical assessment, electrocardiogram (ECG) monitoring, and serial cardiac troponin testing after catecholamine i.v. bolus administration. In case of alterations of these exams, performing a prompt echocardiogram allows early detection of cat-TS, to provide immediate suitable medical support and avoid complications.
Multiple complications of a well-known disease: a case report of acquired Gerbode defect after bicuspid aortic valve endocarditis
Authors: Pereira Sara Couto , Antonio Pedro Silverio , Rigueira Joana , Almeida Ana G 
Published: June 2023

Abstract

Background
Infective endocarditis is a rare but serious disease with high morbidity and mortality due to its potential life-threatening complications. Gerbode defect is an anomalous connection between the left ventricle and the right atrium that can be either congenital or acquired, with previous rare reports following abscess formation in infective endocarditis.

Case summary
A 27-year-old woman presented in hospital with Janeway lesions, stroke, splenic and hepatic abscesses, and transient complete auriculoventricular block. Bicuspid aortic valve infective endocarditis to methicillin-sensitive Staphylococcus aureus and acquired Gerbode defect were diagnosed. After intravenous antibiotics and aortic valve replacement, the patient was discharged without sequelae.

Discussion
Bicuspid aortic valve patients have a higher risk of infective endocarditis than the general population. Infective endocarditis may present with multiple complications, including systemic embolization and local perivalvular lesions. Acquired Gerbode defect is a rare complication of infective endocarditis where transoesophageal echocardiography plays an important role for small shunt detection before surgical intervention.
EUropean real-world outcomes with Pulsed field ablatiOn in patients with symptomatic atRIAl fibrillation: lessons from the multi-centre EU-PORIA registry
Authors: Schmidt Boris , Bordignon Stefano , Neven Kars , Reichlin Tobias , Blaauw Yuri , Hansen Jim , Adelino Raquel , Ouss Alexandre , Füting Anna , Roten Laurent , Mulder Bart A , Ruwald Martin H , Mené Roberto , van der Voort Pepijn , Reinsch Nico , Kueffer Thomas , Boveda Serge , Albrecht Elizabeth M , Schneider Christopher W , Chun Kyoung Ryul Julian 
Published: June 2023

Abstract

Aims
Pulsed field ablation (PFA) is a new, non-thermal ablation modality for pulmonary vein (PV) isolation in patients with atrial fibrillation (AF). The multi-centre EUropean Real World Outcomes with Pulsed Field AblatiOn in Patients with Symptomatic AtRIAl Fibrillation (EU-PORIA) registry sought to determine the safety, efficacy, and learning curve characteristics for the pentaspline, multi-electrode PFA catheter.

Methods and results
All-comer AF patients from seven high-volume centres were consecutively enrolled. Procedural and follow-up data were collected. Learning curve effects were analysed by operator ablation experience and primary ablation modality. In total, 1233 patients (61% male, mean age 66 ± 11years, 60% paroxysmal AF) were treated by 42 operators. In 169 patients (14%), additional lesions outside the PVs were performed, most commonly at the posterior wall (n = 127). Median procedure and fluoroscopy times were 58 (interquartile range: 40–87) and 14 (9–21) min, respectively, with no differences due to operator experience. Major complications occurred in 21/1233 procedures (1.7%) including pericardial tamponade (14; 1.1%) and transient ischaemic attack or stroke (n = 7; 0.6%), of which one was fatal. Prior cryoballoon users had less complication. At a median follow-up of 365 (323–386) days, the Kaplan–Meier estimate of arrhythmia-free survival was 74% (80% for paroxysmal and 66% for persistent AF). Freedom from arrhythmia was not influenced by operator experience. In 149 (12%) patients, a repeat procedure was performed due to AF recurrence and 418/584 (72%) PVs were durably isolated.

Conclusion
The EU-PORIA registry demonstrates a high single-procedure success rate with an excellent safety profile and short procedure times in a real-world, all-comer AF patient population.
Changes in the alcohol-specific disease burden during the COVID-19 pandemic in Germany: interrupted time series analyses
Authors: Manthey Jakob , Kilian Carolin , Schäfer Ingo , Wirth Marielle , Schulte Bernd 
Published: June 2023

Abstract

Background
The coronavirus disease 2019 pandemic has been linked to changes in alcohol consumption, access to healthcare services and alcohol-attributable harm. In this contribution, we quantify changes in alcohol-specific mortality and hospitalizations at the onset of the COVID-19 pandemic in March 2020 in Germany.

Methods
We obtained monthly counts of deaths and hospital discharges between January 2013 and December 2020 (n = 96 months). Alcohol-specific (International Classification of Diseases, tenth revision codes: F10.X; G31.2, G62.1, G72.1, I42.6, K29.2, K70.X, K85.2, K86.0, Q86.0, T51.X) diagnoses were further split into codes reflective of acute vs. chronic harm from alcohol consumption. To quantify the change in alcohol-specific deaths and hospital discharges, we performed sex-stratified interrupted time series analyses using generalized additive mixed models for the population aged 45–74. Immediate (step) and cumulative (slope) changes were considered.

Results
Following March 2020, we observed immediate increases in alcohol-specific mortality among women but not among men. Between the years of 2019 and 2020, we estimate that alcohol-specific mortality among women has increased by 10.8%. Hospital discharges were analyzed separately for acute and chronic conditions. The total number of hospital discharges fell by 21.4% and 25.1% for acute alcohol-specific conditions for women and men, respectively. The total number of hospital discharges for chronic alcohol-specific conditions fell by 7.4% and 8.1% for women and men, respectively.

Conclusions
Increased consumption among people with heavy drinking patterns and reduced utilization of addiction-specific healthcare services during the pandemic might explain excess mortality. During times of public health crises, access to addiction-specific services needs to be ensured.
Xylem function and leaf physiology in European beech saplings during and after moderate and severe drought stress
Authors: Hájíčková Martina , Plichta Roman , Volařík Daniel , Urban Josef , Matoušková Marie , Gebauer Roman 
Published: June 2023

Abstract
The extreme drought events in the last years caused high mortality amongst European beech (Fagus sylvatica L.) across Central Europe. Thus, knowledge of the response of beech to drought and its ability to recover its xylem and leaf functions after drought release is needed to better understand beech survival. In this study, changes in xylem function, leaf gas exchange, chlorophyll fluorescence and morphology of European beech saplings during drought and recovery phases were assessed. Beech saplings were exposed to three different watering intensities—well-watered (W), moderately drought stressed (M) and severely drought stressed (S) for 25 days, and then saplings were rewatered for 14 days. Reduced irrigation caused a drop in shoot water potential to −1.1 and −3.1 MPa in M and S saplings, respectively. Stomatal conductance in M and S saplings decreased to 15 and 5 per cent of that in W saplings, respectively, and it corresponded with a decrease in the photosynthesis rate and chlorophyll fluorescence parameters. Leaf water content and shoot functional xylem area were significantly affected by drought only in S saplings. Hence, these parameters could be used as sensitive indicators that distinguish plants at no risk of mortality from those at increasing risk under drought stress. In S saplings, some leaves also dried from the edges, leaving a green active central part. During the recovery phase, the leaf gas exchange and chlorophyll fluorescence parameters had recovered 4 days after rewatering in M saplings, whereas in S saplings, they were still lower after 2 weeks. Moreover, xylem function did not fully recover in S saplings till the end of the recovery phase. Hence, subsequent drought periods, even of lower intensity, could lead to tree mortality if tree functions have not fully recovered from the previous drought.
Enhancing adaptation of tropical maize to temperate environments using genomic selection
Authors: Choquette Nicole E , Weldekidan Teclemariam , Brewer Jason , Davis Scott B , Wisser Randall J , Holland James B 
Published: June 2023

Abstract
Tropical maize can be used to diversify the genetic base of temperate germplasm and help create climate-adapted cultivars. However, tropical maize is unadapted to temperate environments, in which sensitivities to long photoperiods and cooler temperatures result in severely delayed flowering times, developmental defects, and little to no yield. Overcoming this maladaptive syndrome can require a decade of phenotypic selection in a targeted, temperate environment. To accelerate the incorporation of tropical diversity in temperate breeding pools, we tested if an additional generation of genomic selection can be used in an off-season nursery where phenotypic selection is not very effective. Prediction models were trained using flowering time recorded on random individuals in separate lineages of a heterogenous population grown at two northern U.S. latitudes. Direct phenotypic selection and genomic prediction model training was performed within each target environment and lineage, followed by genomic prediction of random intermated progenies in the off-season nursery. Performance of genomic prediction models was evaluated on self-fertilized progenies of prediction candidates grown in both target locations in the following summer season. Prediction abilities ranged from 0.30 to 0.40 among populations and evaluation environments. Prediction models with varying marker effect distributions or spatial field effects had similar accuracies. Our results suggest that genomic selection in a single off-season generation could increase genetic gains for flowering time by more than 50% compared to direct selection in summer seasons only, reducing the time required to change the population mean to an acceptably adapted flowering time by about one-third to one-half.