bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retrieval of long DNA reads from herbarium specimens
Authors: Quatela Anne-Sophie , Cangren Patrik , Jafari Farzaneh , Michel Thibauld , de Boer Hugo J , Oxelman Bengt 
Published: November 2023

Abstract
High-throughput sequencing of herbarium specimens’ DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (&gt;1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads &gt; 1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads &gt; 1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups.
Role of Peer Support in Building Motivation to Change Addictive Behaviour
Authors: Čtvrtečková Markéta , Stromšíková Alžběta , Roman Lukáš 
Published: November 2023

Abstract
This article deals with the results of a qualitative, multiple-case study that examined the impact of peer support on motivation for change amongst service users in a drug addiction recovery program. A total of nine semi-structured interviews were carried out with patients who also worked with a peer worker as part of their involvement with the service. Participant observation and keeping a research diary were additional methods of data collection. The data collected was further processed using reflective thematic analysis. This article draws on DiClemente’s (2018. Addiction and Change: How Addictions Develop and Addicted People Recover, Guilford Publications) transtheoretical model model of intentional behaviour change and McClelland’s (1951. ‘Personality, Sloane, New York’, in The Achievement Motive, p. 28, New York, Appleton-Century-Crofts) theory of motivation and current research findings on motivation in the context of peer support. Main research question is ‘What mechanisms of formal peer support influence motivation to change harmful behaviour in people who take drugs?’ A key finding is that a successfully established peer-service user relationship is a key instrument and premise for building motivation for change. It also presents an overview of the basic mechanisms that build the peer-service user relationship as well as the basic mechanisms that build motivation for change. It is concluded by a discussion on these mechanisms and the current literature as well as drawing implications for practice.
Three out of one: revising the species delimitation of the tree fern Gymnosphaera salletii (Cyatheaceae), with particular reference to the foliar nectary
Authors: Li Shu-Han , Zuo Zheng-Yu , Chen Cheng-Wei , Pham Van The , Luu Hong Truong , Dong Shi-Yong 
Published: November 2023

Abstract
In Indochina the species diversity of Cyatheaceae remains insufficiently known. Here we demonstrate the scaly tree fern Gymnosphaera salletii in Vietnam to be an assemblage of three distinct species based on molecular and morphological data, and report for the first time the occurrence of foliar nectaries in Gymnosphaera. The true G. salletii is morphologically unique based on the protuberant glands present on the petiole. Gymnosphaera phankelocii sp. nov. and Gymnosphaeravietnamensis sp. nov. are recognized as new species; G. phankelocii is characterized by its distant two-rowed sori and G. vietnamensis by the sub-tripinnate fronds. Our phylogenetic analyses indicated that G. phankelocii is a relatively isolated species, while G. vietnamensis is a member of the G. salletii clade along with G. austroyunnanensis, G. salletii, and G. saxicola. The two new species and members of the G. salletii clade are all local endemics, and provide good examples to understand the frequent local endemics and their evolution in scaly tree ferns. Eleven species of Gymnosphaera are now known from Indochina; we provide a diagnostic key to these species.
Effects of climatic fluctuations on the fragmented distribution pattern of a Tertiary relict plant, Pseudotaxus chienii (Taxaceae), in subtropical China
Authors: Li Ning , Wang Zhen , Deng Qi , Wang Ting , Su Ying-Juan 
Published: November 2023

Abstract
Habitat fragmentation can facilitate local adaptation of species to heterogeneous environments and affect population demographic history. To understand the factors influencing evolutionary dynamics, such as climatic fluctuations and complex geomorphological features, we used 18 chloroplast microsatellites, 15 nuclear microsatellites, three chloroplast fragments, and two nuclear regions to explore the genetic structure and phylogeographical history of Pseudotaxus chienii. Furthermore, its current and past distributions were constructed based on ecological niche modelling. Moderate to high levels of genetic diversity were found at the species level. Precipitation was a decisive factor influencing the genetic structure of P. chienii. In addition, local adaptation to heterogeneous environments also contributed to maintain the fragmented distribution. Finally, incomplete lineage sorting led to the cyto-nuclear discordance. Overall, we show that pre-Quaternary and Quaternary climatic fluctuations and restricted gene flow exerted significant effects on the formation and maintenance of the fragmented distribution of P. chienii. The study provides new insights into the evolutionary history of plants in subtropical China.
Comparison of the effects of peritoneal dialysis and hemodialysis on spontaneous brain activity in CKD patients: an rs-fMRI study
Authors: Zhang Chaoyang , Cai Yan , Yu Huan , Wu Ning , Liu Jiexi , Liang Shuang , Zhang Chun , Duan Zhiyu , Zhang Zhou , Cai Guangyan 
Published: November 2023

Abstract

Objective
To compare the effects of peritoneal dialysis and hemodialysis on spontaneous brain activity in patients with end-stage renal disease.

Methods
A total of 52 dialysis patients with end-stage renal disease, including 25 patients with chronic kidney disease undergoing hemodialysis (HD-CKD) and 27 patients with chronic kidney disease undergoing peritoneal dialysis (PD-CKD), and 49 healthy controls (normal control) were included. All participants underwent neuropsychological testing (Mini-Mental State Examination and Montreal cognitive assessment) and resting-state functional magnetic resonance imaging. Fractional amplitude of low frequency fluctuations and Regional Homogeneity algorithms were employed to evaluate spontaneous brain activity. Statistical analysis was performed to discern differences between the groups.

Results
When compared with the normal control group, the PD-CKD group exhibited significant alterations in fractional amplitude of low frequency fluctuations in various cerebellum regions and other brain areas, while the HD-CKD group showed decreased fractional amplitude of low frequency fluctuations in the bilateral pericalcarine cortex. The Regional Homogeneity values in the PD-CKD group were notably different than those in the normal control group, particularly in regions such as the bilateral caudate nucleus and the right putamen.

Conclusion
Both peritoneal dialysis and hemodialysis modalities impact brain activity, but manifest differently in end-stage renal disease patients. Understanding these differences is crucial for optimizing patient care.
Characterizing microstructural development in the fetal brain using diffusion MRI from 23 to 36 weeks of gestation
Authors: Calixto Camilo , Machado-Rivas Fedel , Cortes-Albornoz Maria C , Karimi Davood , Velasco-Annis Clemente , Afacan Onur , Warfield Simon K , Gholipour Ali , Jaimes Camilo 
Published: November 2023

Abstract
We utilized motion-corrected diffusion tensor imaging (DTI) to evaluate microstructural changes in healthy fetal brains during the late second and third trimesters. Data were derived from fetal magnetic resonance imaging scans conducted as part of a prospective study spanning from 2013 March to 2019 May. The study included 44 fetuses between the gestational ages (GAs) of 23 and 36 weeks. We reconstructed fetal brain DTI using a motion-tracked slice-to-volume registration framework. Images were segmented into 14 regions of interest (ROIs) through label propagation using a fetal DTI atlas, with expert refinement. Statistical analysis involved assessing changes in fractional anisotropy (FA) and mean diffusivity (MD) throughout gestation using mixed-effects models, and identifying points of change in trajectory for ROIs with nonlinear trends. Results showed significant GA-related changes in FA and MD in all ROIs except in the thalamus’ FA and corpus callosum’s MD. Hemispheric asymmetries were found in the FA of the periventricular white matter (pvWM), intermediate zone, and subplate and in the MD of the ganglionic eminence and pvWM. This study provides valuable insight into the normal patterns of development of MD and FA in the fetal brain. These changes are closely linked with cytoarchitectonic changes and display indications of early functional specialization.
Cortical microstructural brain network mediates the association between personality trait of agreeableness and life satisfaction
Authors: Wu Huijun , Fan Shijia , Yan Chuyao , Wang Hao 
Published: November 2023

Abstract
Personality traits are commonly regarded as relatively stable, whereas life satisfaction can fluctuate with time and circumstances, shaped by external influences and personal encounters. The correlation between personality traits and life satisfaction is well-established, yet the underlying neural mechanisms of the myelin-based microstructural brain network connecting them remain unclear. Here, we constructed individual-level whole-brain myelin microstructural networks from the MRI data of 1,043 healthy adults and performed correlation analysis to detect significant personality trait-related and life satisfaction-related subnetworks. A mediation analysis was used to verify whether the shared structural basis of personality traits and life satisfaction significantly mediated their association. The results showed that agreeableness positively correlated with life satisfaction. We identified a shared structural basis of the personality trait of agreeableness and life satisfaction. The regions comprising this overlapping network include the superior parietal lobule, inferior parietal lobule, and temporoparietal junction. Moreover, the shared microstructural connections mediate the association between the personality trait of agreeableness and life satisfaction. This large-scale neuroimaging investigation substantiates a mediation framework for understanding the microstructural connections between personality and life satisfaction, offering potential targets for assessment and interventions to promote human well-being.
Age-associated cortical similarity networks correlate with cell type-specific transcriptional signatures
Authors: Niu Jinpeng , Jiao Qing , Cui Dong , Dou Ruhai , Guo Yongxin , Yu Guanghui , Zhang Xiaotong , Sun Fengzhu , Qiu Jianfeng , Dong Li , Cao Weifang 
Published: November 2023

Abstract
Human brain structure shows heterogeneous patterns of change across adults aging and is associated with cognition. However, the relationship between cortical structural changes during aging and gene transcription signatures remains unclear. Here, using structural magnetic resonance imaging data of two separate cohorts of healthy participants from the Cambridge Centre for Aging and Neuroscience (n = 454, 18–87 years) and Dallas Lifespan Brain Study (n = 304, 20–89 years) and a transcriptome dataset, we investigated the link between cortical morphometric similarity network and brain-wide gene transcription. In two cohorts, we found reproducible morphometric similarity network change patterns of decreased morphological similarity with age in cognitive related areas (mainly located in superior frontal and temporal cortices), and increased morphological similarity in sensorimotor related areas (postcentral and lateral occipital cortices). Changes in morphometric similarity network showed significant spatial correlation with the expression of age-related genes that enriched to synaptic-related biological processes, synaptic abnormalities likely accounting for cognitive decline. Transcription changes in astrocytes, microglia, and neuronal cells interpreted most of the age-related morphometric similarity network changes, which suggest potential intervention and therapeutic targets for cognitive decline. Taken together, by linking gene transcription signatures to cortical morphometric similarity network, our findings might provide molecular and cellular substrates for cortical structural changes related to cognitive decline across adults aging.
Efficacy of Bortezomib for Treating Anti-Interferon-Gamma Autoantibody-Associated Adult-Onset Immunodeficiency Syndrome
Authors: Angkasekwinai Nasikarn , Suputtamongkol Yupin , Tantibhedhyangkul Wiwit , Onlamoon Nattawat , Phoompoung Pakpoom , Pithukpakorn Manop , Karuphong Ekkapun , Pusuwan Pawana , Angkasekwinai Pornpimon 
Published: November 2023

Abstract

Background
Currently, there is no effective treatment for adult-onset immunodeficiency (AOID) syndrome with anti-interferon-gamma autoantibodies (anti-IFN-γ-auto-Abs). This study aimed to investigate the effectiveness of bortezomib (BTZ) for decreasing anti-IFN-γ-auto-Abs.

Methods
A pre- and post-intervention study was conducted from February 2017 through June 2019 at Siriraj Hospital (Bangkok, Thailand). Five patients were invited to receive once-weekly BTZ (1.3 mg/m2 body surface area) subcutaneously for 8 weeks followed by oral cyclophosphamide (1 mg/kg/d) for 4 months. The primary outcomes were the difference in antibody level at 8 and 48 weeks compared with baseline and the incidence of serious adverse events (AEs). The secondary outcome was the occurrence of opportunistic infections (OIs) during the 72 weeks after starting BTZ.

Results
The median patient age was 46 years (range, 34–53). All patients had 3–5 OIs prior to enrollment. All patients were receiving antimycobacterial agents for treatment of nontuberculous mycobacterial infection at enrollment. There was no significant difference in the mean optical density of auto-Abs at 8 weeks (3.73 ± 0.72) or 48 weeks (3.74 ± 0.53) compared with baseline (3.84 ± 0.49; P = .336 and P = .555, respectively). However, after serum dilution, the antibody titer nonsignificantly decreased 8–16 weeks after BTZ initiation (P = .345). Ten OIs were observed 24–72 weeks after BTZ initiation.

Conclusions
Treatment with BTZ followed by cyclophosphamide yielded no significant decrease in antibody titer levels, and 10 OIs were observed during 24–72 weeks of BTZ treatment. No serious AEs were observed. Combining rituximab with BTZ is likely necessary to prevent generation of new autoantibody-producing plasma cells.
Clinical Trials Registration. NCT03103555.
Brain Abscess Caused by Oral Cavity Bacteria: A Nationwide, Population-based Cohort Study
Authors: Bodilsen Jacob , Mariager Theis , Duerlund Lærke Storgaard , Storgaard Merete , Larsen Lykke , Brandt Christian Thomas , Hansen Birgitte Rønde , Wiese Lothar , Omland Lars Haukali , Nielsen Henrik ,   Danish Study Group of Infections of the Brain, Storgaard Merete , Larsen Lykke , Hansen Birgitte Rønde , Andersen Christian Østergaard , Wiese Lothar , Jepsen Micha Phill Grønholm , Mens Helene , Lüttichau Hans Rudolf , Nielsen Henrik , Bodilsen Jacob 
Published: November 2023

Abstract

Background
Oral cavity bacteria are the most frequent etiology of brain abscess. Yet, data on the clinical presentation and outcome are scarce.

Methods
We performed a nationwide, population-based study comprising all adults (aged ≥18 years) with brain abscess due to oral cavity bacteria in Denmark from 2007 through 2020. Prognostic factors for unfavorable outcome (Glasgow outcome scale, 1–4) were examined using modified Poisson regression to compute adjusted relative risks (RRs) with 95% confidence intervals (CIs).

Results
Among 287 identified patients, the median age was 58 years (interquartile range, 47–66), and 96 of 287 (33%) were female. Preexisting functional impairment was absent or mild in 253 of 280 (90%), and risk factors for brain abscess included immunocompromise in 95 of 287 (33%), dental infection in 68 of 287 (24%), and ear–nose–throat infection in 33 of 287 (12%). Overall, a neurological deficit was present in 246 of 276 (86%) and in combination with headache and fever in 64 of 287 (22%). Identified microorganisms were primarily the Streptococcus anginosus group, Fusobacterium, Actinomyces, and Aggregatibacter spp., and 117 of 287 (41%) were polymicrobial. Unfavorable outcome occurred in 92 of 246 (37%) at 6 months after discharge and was associated with antibiotics before neurosurgery (RR, 3.28; 95% CI, 1.53–7.04), rupture (RR, 1.89; 95% CI, 1.34–2.65), and immunocompromise (RR, 1.80; 95% CI, 1.29–2.51), but not with specific targeted antibiotic regimens. Identified dental infection was associated with favorable prognosis (RR, 0.58; 95% CI, .36–.93).

Conclusions
Brain abscess due to oral cavity bacteria often occurred in previously healthy individuals without predisposing dental infections. Important risk factors for unfavorable outcome were rupture and immunocompromise. However, outcome was not associated with specific antibiotic regimens supporting carbapenem-sparing strategies.
Incremental versus conventional haemodialysis in end-stage kidney disease: a systematic review and meta-analysis
Authors: Takkavatakarn Kullaya , Jintanapramote Kavita , Phannajit Jeerath , Praditpornsilpa Kearkiat , Eiam-Ong Somchai , Susantitaphong Paweena 
Published: November 2023

ABSTRACT

Background
Appropriate dialysis prescription in the transitional setting from chronic kidney disease to end-stage kidney disease is still challenging. Conventional thrice-weekly haemodialysis (HD) might be associated with rapid loss of residual kidney function (RKF) and high mortality. The benefits and risks of incremental HD compared with conventional HD were explored in this systematic review and meta-analysis.

Methods
We searched MEDLINE, Scopus and Cochrane Central Register of Controlled Trials up to April 2023 for studies that compared the impacts of incremental (once- or twice-weekly HD) and conventional thrice-weekly HD on cardiovascular events, RKF, vascular access complications, quality of life, hospitalization and mortality.

Results
A total of 36 articles (138 939 participants) were included in this meta-analysis. The mortality rate and cardiovascular events were similar between incremental and conventional HD {odds ratio [OR] 0.87 [95% confidence interval (CI)] 0.72–1.04 and OR 0.67 [95% CI 0.43–1.05], respectively}. However, hospitalization and loss of RKF were significantly lower in patients treated with incremental HD [OR 0.44 (95% CI 0.27–0.72) and OR 0.31 (95% CI 0.25–0.39), respectively]. In a sensitivity analysis that included studies restricted to those with RKF or urine output criteria, incremental HD had significantly lower cardiovascular events [OR 0.22 (95% CI 0.08–0.63)] and mortality [OR 0.54 (95% CI 0.37–0.79)]. Vascular access complications, hyperkalaemia and volume overload were not statistically different between groups.

Conclusions
Incremental HD has been shown to be safe and may provide superior benefits in clinical outcomes, particularly in appropriately selected patients. Large-scale randomized controlled trials are required to confirm these potential advantages.
API Recommendation For Mashup Creation: A Comprehensive Survey
Authors: Alhosaini Hadeel , Alharbi Sultan , Wang Xianzhi , Xu Guandong 
Published: November 2023

AbstractMashups are web applications that expedite software development by reusing existing resources through integrating multiple application programming interfaces (APIs). Recommending the appropriate APIs plays a critical role in assisting developers in building such web applications easily and efficiently. The proliferation of publicly available APIs on the Internet has inspired the community to adopt various models to accomplish the recommendation task. Until present, considerable efforts have been made to recommend the optimal set of APIs, delivering fruitful results and achieving varying recommendation performance. This paper presents a timely review on the topic of API recommendations for mashup creation. Specifically, we investigate and compare not only traditional data mining approaches and recommendation techniques but also more recent approaches based on network representation learning and deep learning techniques. By analyzing the merits and pitfalls of existing approaches, we pinpoint a few promising directions to address the remaining challenges in the current research. This survey provides a timely comprehensive review of the API recommendation research and could be a useful reference for relevant researchers and practitioners.
Role of conduction system pacing in ablate and pace strategies for atrial fibrillation
Authors: Tung Roderick , Burri Haran 
Published: November 2023

Abstract
With the advent of conduction system pacing, the threshold for performing ‘ablate and pace’ procedures for atrial fibrillation has gone down markedly in many centres due to the ability to provide a simple and physiological means of pacing the ventricles. This article reviews the technical considerations for this strategy as well as the current evidence, recognized indications, and future perspectives.
On a collision course: fatal motorcycle and bicycle accidents of adolescents in Finland from 2008 to 2019
Authors: Unkuri Jani , Salminen Päivi , Sihvola Niina , Kosola Silja 
Published: November 2023

Abstract

Background
Transport injuries are a major cause of mortality among adolescents. Our aim was to evaluate the circumstances and trauma associated with fatal accidents involving adolescents and two-wheeled vehicles.

Methods
We analyzed retrospective data from the Finnish Crash Data Institute from 2008 to 2019 involving 10- to 24-year-old victims of fatal traffic accidents who were injured while riding a bicycle, moped or motorcycle. We collected data on patient characteristics, accident circumstances and possible treatment. These fatalities were compared with national mortality rates among the respective age groups.

Results
We identified 147 fatalities over the 12-year period involving 20 bicycle, 50 moped and 77 motorcycle riders. Most accidents involved males (n = 121, 82%). Less than half of vehicles were in good condition (46%); motorized vehicles were often illegally tuned (37%) or had tire problems (31%). Most of the accidents were collisions with another vehicle (n = 99, 67%) or other objects (n = 35, 24%). In 94% of cases, the Injury Severity Score was &gt;25. Head injury was the most common cause of death (62%). Among 15-year-olds, every fifth death was due to accidents on two-wheeled vehicles.

Conclusions
Fatal transport accidents among adolescents comprise several elements that should be incorporated into driver’s education and in case of minors, also communicated to parents. These include the condition of the vehicle, proper helmet use and effects of speed on both control of the vehicle and the consequences of a possible collision.