bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lag penalized weighted correlation for time series clustering
Authors: Chandereng Thevaa , Gitter Anthony 
Published: January 2020

AbstractBackgroundThe similarity or distance measure used for clustering can generate intuitive and interpretable clusters when it is tailored to the unique characteristics of the data. In time series datasets generated with high-throughput biological assays, measurements such as gene expression levels or protein phosphorylation intensities are collected sequentially over time, and the similarity score should capture this special temporal structure.ResultsWe propose a clustering similarity measure called Lag Penalized Weighted Correlation (LPWC) to group pairs of time series that exhibit closely-related behaviors over time, even if the timing is not perfectly synchronized. LPWC aligns time series profiles to identify common temporal patterns. It down-weights aligned profiles based on the length of the temporal lags that are introduced. We demonstrate the advantages of LPWC versus existing time series and general clustering algorithms. In a simulated dataset based on the biologically-motivated impulse model, LPWC is the only method to recover the true clusters for almost all simulated genes. LPWC also identifies clusters with distinct temporal patterns in our yeast osmotic stress response and axolotl limb regeneration case studies.ConclusionsLPWC achieves both of its time series clustering goals. It groups time series with correlated changes over time, even if those patterns occur earlier or later in some of the time series. In addition, it refrains from introducing large shifts in time when searching for temporal patterns by applying a lag penalty. The LPWC R package is available athttps://github.com/gitter-lab/LPWCand CRAN under a MIT license.
Current status and factors influencing oral anticoagulant therapy among patients with non-valvular atrial fibrillation in Jiangsu province, China: a multi-center, cross-sectional study
Authors: Liu Ting , Yang Hui-li , Gu Lan , Hui Jie , Omorogieva Ojo , Ren Meng-xiao , Wang Xiao-hua 
Published: January 2020

Abstract
Background
It has been reported that oral anticoagulation (OAC) is underused among Chinese patients with non-valvular atrial fibrillation (NVAF). Non-vitamin K antagonist oral anticoagulants (NOAC) have been recommended by recent guidelines and have been covered since 2017 by the Chinese medical insurance; thus, the overall situation of anticoagulant therapy may change. The aim of this study was to explore the current status of anticoagulant therapy among Chinese patients with NVAF in Jiangsu province.

Methods
This was a multi-center, cross-sectional study that was conducted in seven hospitals from January to September in 2017. The demographic characteristics and medical history of the patients were collected by questionnaire and from the medical records. Multivariate logistic regression was used to identify factors associated with anticoagulant therapy.

Results
A total of 593 patients were included in the analysis. A total of 35.6% of the participants received OAC (11.1% NOAC and 24.5% warfarin). Of those patients with a high risk of stroke, 11.1% were on NOAC, 24.8% on warfarin, 30.6% on aspirin, and 33.6% were not on medication. Self-paying, duration of AF ≥5 years were negatively associated with anticoagulant therapy in all patients (OR 1.724, 95% CI 1.086~2.794; OR 1.471, 95% CI 1.006~2.149, respectively), whereas, permanent AF was positively associated with anticoagulant therapy (OR 0.424, 95% CI 0.215~0.839). Among patients with high risk of stroke, self-paying and increasing age were negatively associated with anticoagulant therapy (OR 2.305, 95% CI 1.186~4.478; OR 1.087, 95% CI 1.041~1.135, respectively).

Conclusions
Anticoagulant therapy is positively associated with permanent AF and negatively associated with self-paying, duration of AF > 5 years. Furthermore, the current status of anticoagulant therapy among Chinese patients with NVAF in Jiangsu province does not appear optimistic. Therefore, further studies should focus on how to improve the rate of OAC use among NVAF patients. In addition, policy makers should pay attention to the economic situation of the patients with NVAF using NOAC.

Trial registration
2,017,029. Registered 20 March 2017 (retrospectively registered).
Comorbid status and the faecal microbial transplantation failure in treatment of recurrent Clostridioides difficile infection – pilot prospective observational cohort study
Authors: Kachlíková M. , Sabaka P. , Koščálová A. , Bendžala M. , Dovalová Z. , Stankovič I. 
Published: January 2020

Abstract
Background
Faecal microbial transplantation (FMT) is currently the most effective treatment of recurrent Clostridioides difficile infection (CDI). However, up to 20% of patients experience further recurrences after single FMT. The mechanisms that lead to FMT failure and its risk factors are poorly understood. Comorbidity is one of the risk factors of the failure of standard antibiotic therapy of recurrent CDI. It is not known if comorbidity is also associated with the risk of FMT failure.

Methods
We conducted a prospective observational cohort study in order to elucidate if comorbid status is associated with FMT failure. Patients with microbiologically proven recurrent CDI were recruited and underwent FMT via retention enema. Patients were followed up for 12 weeks after FMT for signs and symptoms of CDI recurrence. Single FMT failure was defined as recurrence of diarrhoea and a positive stool test for the presence of C. difficile antigen or toxin at any time point during the 12 weeks of follow-up. We assessed the association of single FMT failure with possible manageable and unmanageable risk factors. As a surrogate of comorbid status, we used Charlson Comorbidity Index (CCI) ≥ 7.

Results
A total of 60 patients that underwent single FMT (34 women, 26 men) were included in the study. Overall, 15 patients (25%) experienced single FMT failure. 24 patients (40%) had CCI ≥ 7, and 45.0% patients with CCI ≥ 7 experienced failure of single FMT. Patients who experienced single FMT failure had a significantly higher CCI and significantly lower albumin concentration as compared to patients who experienced single FMT success. There was no difference in age, C-reactive protein concentration, leukocyte count and time from FMT to first defecation. In multivariate analysis, CCI ≥ 7 was positively associated with the failure of single FMT. Analysis was controlled for sex, age, time from FMT to first defecation, concomitant PPI therapy, severe CDI, hospital-acquired infection and albumin concentration.

Conclusions
Comorbid status surrogated by CCI is positively associated with the failure of single FMT in the treatment of recurrent CDI.
A new approach to characterize postural deficits in chemotherapy-induced peripheral neuropathy and to analyze postural adaptions after an exercise intervention
Authors: Kneis Sarah , Wehrle Anja , Dalin Daniela , Wiesmeier Isabella Katharina , Lambeck Johann , Gollhofer Albert , Bertz Hartmut , Maurer Christoph 
Published: January 2020

Abstract
Background
Postural instability presents a common and disabling consequence of chemotherapy-induced peripheral neuropathy (CIPN). However, knowledge about postural behavior of CIPN patients is sparse. With this pilot study, we used a new approach to i) characterize postural impairments as compared to healthy subjects, ii) allocate possible abnormalities to a set of parameters describing sensorimotor function, and iii) evaluate the effects of a balance-based exercise intervention.

Methods
We analyzed spontaneous and externally perturbed postural control in eight CIPN patients before and after a balance-based exercise intervention by using a modification of an established postural control model. These findings were compared to 15 matched healthy subjects.

Results
Spontaneous sway amplitude and velocity were larger in CIPN patients compared to healthy subjects. CIPN patients’ reactions to external perturbations were smaller compared to healthy subjects, indicating that patients favor vestibular over proprioceptive sensory information. The balance-based exercise intervention up-weighted proprioceptive information in patients.

Conclusions
CIPN patients’ major postural deficit may relate to underuse of proprioceptive information that results in a less accurate posture control as spontaneous sway results indicate. The balance-based exercise intervention is able to partially correct for this abnormality. Our study contributes to a better understanding of postural impairments in CIPN patients and suggests an effective treatment strategy.

Trial registration
German Clinical Trials Register: DRKS00004340, retrospectively registered 04 January 2013.
Exploring preconception health beliefs amongst adults of childbearing age in the UK: a qualitative analysis
Authors: McGowan Laura , Lennon-Caughey Emer , Chun Cheryl , McKinley Michelle C. , Woodside Jayne V. 
Published: January 2020

Abstract
Background
‘Preconception health’ or ‘pre-pregnancy health’ are terms used to describe the health status of males and females prior to pregnancy. The goal of preconception health strategies is to optimise the health of future offspring via improved parental health, which may result from planned/unplanned pregnancies. Greater emphasis is being placed upon preconception health amongst research and public health, yet there is limited evidence on this topic from the perspective of UK adults. This research explored beliefs, knowledge and attitudes on preconception health amongst adults of childbearing age, drawn from the UK.

Methods
A descriptive qualitative focus group study was undertaken with healthy males and females of childbearing age (18–45 years) between October 2018 and July 2019. Two groups were held in a rural location (one focus group, one mini focus group) and three groups held in an urban location (two focus groups, one mini focus group), with a range of males and females, with and without children. A semi-structured topic guide was devised based on previous literature. All groups were conducted with two researchers trained in qualitative research methods. Focus groups explored understanding/prior knowledge of preconception health, beliefs and attitudes towards preconception healthcare support and personal health. Focus groups were transcribed verbatim and analysed using thematic analysis.

Results
Twenty-one males and females of childbearing age (aged 18 to 45 years) participated in the research. Discussions revealed a lack of comprehensive awareness of the importance of preconception health and a sense of reluctance to visit a doctor regarding the issue, favouring the internet, unless having problems conceiving. Five themes identified included: preconception education, preconception awareness, wider knowledge networks/support, optimal parental health, and attitudes/emotions towards preconception health. The roles of males regarding positive preconception care was not well understood.

Conclusions
This study highlighted a lack of detailed awareness surrounding the importance of preconception health per se, despite general agreement that health status should be optimal at this time. It identified a willingness to learn more about preconception health, creating an opportunity to improve preconception healthcare awareness via evidence-based education, social media campaigns, and within healthcare systems in a life course approach.
Bacteriocin production by mucosal bacteria in current and previous colorectal neoplasia
Authors: Kohoutova Darina , Forstlova Miroslava , Moravkova Paula , Cyrany Jiri , Bosak Juraj , Smajs David , Rejchrt Stanislav , Bures Jan 
Published: January 2020

Abstract
Background
Optimal therapy for colorectal carcinoma (CRC), a frequently diagnosed malignancy, does not exist. Some of colicins and microcins, ribosomally synthesized peptides by gramnegative bacteria, have shown significant biological activity specifically against different cancer cells in vitro and in vivo conditions. The aim of this prospective study was to evaluate natural colicin and microcin production by large intestinal mucosal bacteria in each stage of colorectal neoplasia and in those with a history of colorectal neoplasia.

Methods
A total of 21 patients with non-advanced adenoma (non-a-A; 16/21 with current and 5/21 with history of non-a-A), 20 patients with advanced colorectal adenoma (a-A; 11/20 with current and 9/20 with history of a-A), 22 individuals with CRC (9/22 with current and 13/22 with history of CRC) and 20 controls were enrolled. Mucosal biopsies from the caecum, transverse colon and the rectum were taken during colonoscopy in each individual. Microbiological culture followed. Production of colicins and microcins was evaluated by PCR methods.

Results
A total of 239 mucosal biopsies were taken. Production of colicins and microcins was significantly more frequent in individuals with non-a-A, a-A and CRC compared to controls. No significant difference in colicin and microcin production was found between patients with current and previous non-a-A, a-A and CRC. Significantly more frequent production of colicins was observed in men compared to women at the stage of colorectal carcinoma. A later onset of increased production of microcins during the adenoma-carcinoma sequence has been observed in males compared to females.

Conclusions
Strains isolated from large intestinal mucosa in patients with colorectal neoplasia produce colicins and microcins more frequently compared to controls. Bacteriocin production does not differ between patients with current and previous colorectal neoplasia. Fundamental differences in bacteriocin production have been confirmed between males and females.
Comprehensive profiling of circular RNA expressions reveals potential diagnostic and prognostic biomarkers in multiple myeloma
Authors: Zhou Fan , Wang Dongjiao , Wei Wei , Chen Haimin , Shi Haotian , Zhou Nian , Wu Lixia , Peng Rong 
Published: January 2020

Abstract
Background
This study aimed to explore the heterogeneity of circRNA expression pattern via microarray, and further evaluate the potential of 10 specific circRNAs as diagnostic and prognostic biomarkers in multiple myeloma (MM).

Methods
In exploration stage (stage I), circRNA expression profiles were detected by the microarray in bone marrow plasma cells from 4 MM patients and 4 healthy controls (HCs), and bioinformatic analyses were performed. In validation stage (stage II), top 10 upregulated and top 10 downregulated circRNAs identified in stage I were detected in 60 MM patients and 30 HCs for further validation; the diagnostic and prognostic values of these circRNAs in MM patients were analyzed.

Results
In stage I, 122 upregulated and 260 downregulated circRNAs were identified in MM patients compared with HCs. GO, KEGG and pathway enrichment analyses revealed that these circRNAs were implicated in neoplastic pathways such as MAPK and VEGF signaling pathways. In stage II, circ-PTK2, circ-RNF217, circ-RERE, circ-NAGPA and circ-KCNQ5 were validated to be upregulated and circ-AFF2, circ-WWC3, circ-DNAJC5, circ-KLHL2, circ-IQGAP1 and circ-AL137655 were validated to be downregulated in MM compared with controls. Circ-PTK2 and circ-RNF217 were correlated with poor treatment response and survival, while circ-AFF2 predicted good treatment response and survival in MM patients.

Conclusions
This study provides valuable reference for profound understanding about circRNA expression patterns in MM, and validates that circ-PTK2, circ-RNF217 and circ-AFF2 might serve as potential prognostic biomarkers in MM.
Medicinal cannabis for psychiatric disorders: a clinically-focused systematic review
Authors: Sarris Jerome , Sinclair Justin , Karamacoska Diana , Davidson Maggie , Firth Joseph 
Published: January 2020

AbstractBackgroundMedicinal cannabis has received increased research attention over recent years due to loosening global regulatory changes. Medicinal cannabis has been reported to have potential efficacy in reducing pain, muscle spasticity, chemotherapy-induced nausea and vomiting, and intractable childhood epilepsy. Yet its potential application in the field of psychiatry is lesser known.MethodsThe first clinically-focused systematic review on the emerging medical application of cannabis across all major psychiatric disorders was conducted. Current evidence regarding whole plant formulations and plant-derived cannabinoid isolates in mood, anxiety, sleep, psychotic disorders and attention deficit/hyperactivity disorder (ADHD) is discussed; while also detailing clinical prescription considerations (including pharmacogenomics), occupational and public health elements, and future research recommendations. The systematic review of the literature was conducted during 2019, assessing the data from all case studies and clinical trials involving medicinal cannabis or plant-derived isolates for all major psychiatric disorders (neurological conditions and pain were omitted).ResultsThe present evidence in the emerging field of cannabinoid therapeutics in psychiatry is nascent, and thereby it is currently premature to recommend cannabinoid-based interventions. Isolated positive studies have, however, revealed tentative support for cannabinoids (namely cannabidiol; CBD) for reducing social anxiety; with mixed (mainly positive) evidence for adjunctive use in schizophrenia. Case studies suggest that medicinal cannabis may be beneficial for improving sleep and post-traumatic stress disorder, however evidence is currently weak. Preliminary research findings indicate no benefit for depression from high delta-9 tetrahydrocannabinol (THC) therapeutics, or for CBD in mania. One isolated study indicates some potential efficacy for an oral cannabinoid/terpene combination in ADHD. Clinical prescriptive consideration involves caution in the use of high-THC formulations (avoidance in youth, and in people with anxiety or psychotic disorders), gradual titration, regular assessment, and caution in cardiovascular and respiratory disorders, pregnancy and breast-feeding.ConclusionsThere is currently encouraging, albeit embryonic, evidence for medicinal cannabis in the treatment of a range of psychiatric disorders. Supportive findings are emerging for some key isolates, however, clinicians need to be mindful of a range of prescriptive and occupational safety considerations, especially if initiating higher dose THC formulas.
High tuberosity healing rate associated with better functional outcome following primary reverse shoulder arthroplasty for proximal humeral fractures with a 135° prosthesis
Authors: Schmalzl Jonas , Jessen Malik , Sadler Nadine , Lehmann Lars-Johannes , Gerhardt Christian 
Published: January 2020

Abstract
Background
Reverse shoulder arthroplasty (RSA) is a common treatment for proximal humeral fractures. (PHF) in the elderly. This study evaluates the functional outcome and the influence of. tuberosity healing (TH) following RSA with 135° humeral inclination and a neutral glenosphere without lateralization for PHFs.

Methods
In this retrospective case series, all patients with an acute PHF treated with primary RSA with 135° humeral inclination and a standard glenosphere without lateralization during a four-year period were followed up. Constant score (CS), patient satisfaction (subjective shoulder value (SSV)), TH and glenoid notching were analyzed.

Results
38 patients with a mean age of 77 ± 8 years were available for follow-up at 34 ± 5 months. The mean adjusted CS was 61 ± 9 points. TH of the greater tuberosity (GT) was 82% and resulted in significantly improved abduction (117° vs. 81°; P < 0.001), forward flexion (139° vs. 99°; p < 0.001), external rotation (28° vs. 10°; p = 0.002), CS (65 vs. 41 points; p < 0.001) and patient satisfaction (SSV 79% vs. 48%; p < 0.001). TH of the LT was 87% without affecting internal rotation or overall outcome. The complication- and revision rate was 5%; implant survival was 100%. Scapular notching occurred in 3 (8%) cases (all grade 1).

Conclusion
RSA with 135° humeral inclination and a standard glenosphere for PHF leads to good functional outcome in combination with a high rate of TH and a low rate of scapular notching. The short-term revision rate is low and the results are predictable and continuous. TH is associated with improved ROM, patient satisfaction and functional outcome.
Evaluating DREAMS HIV prevention interventions targeting adolescent girls and young women in high HIV prevalence districts in South Africa: protocol for a cross-sectional study
Authors: George Gavin , Cawood Cherie , Puren Adrian , Khanyile David , Gerritsen Annette , Govender Kaymarlin , Beckett Sean , Glenshaw Mary , Diallo Karidia , Ayalew Kassahun , Gibbs Andrew , Reddy Tarylee , Madurai Lorna , Kufa-Chakezha Tendesayi , Kharsany Ayesha B. M. 
Published: January 2020

Abstract
Background
Young women in sub-Saharan Africa remain at the epicentre of the HIV epidemic, with surveillance data indicating persistent high levels of HIV incidence. In South Africa, adolescent girls and young women (AGYW) account for a quarter of all new HIV infections. Determined, Resilient, Empowered, AIDS-free, Mentored and Safe (DREAMS) is a strategy introduced by the United States President’s Emergency Plan for AIDS Relief (PEPFAR) aimed at reducing HIV incidence among AGYW in 10 countries in sub-Saharan Africa by 25% in the programme’s first year, and by 40% in the second year. This study will assess the change in HIV incidence and reduction in risk associated behaviours that can be attributed to the DREAMS initiative in South Africa, using a population-based cross-sectional survey.

Methods
Data will be collected from a household-based representative sample of AGYW (between the ages 12–24 years) in four high prevalence districts (more than 10% of the population have HIV in these districts) in South Africa in which DREAMS has been implemented. A stratified cluster-based sampling approach will be used to select eligible participants for a cross-sectional survey with 18,500, to be conducted over 2017/2018. A questionnaire will be administered containing questions on sexual risk behaviour, selected academic and developmental milestones, prevalence of gender based violence, whilst examining exposure to DREAMS programmes. Biological samples, including two micro-containers of blood and self-collected vulvovaginal swab samples, are collected in each survey to test for HIV infection, HIV incidence, sexually transmitted infections (STIs) and pregnancy. This study will measure trends in population level HIV incidence using the Limiting antigen (LAg) Avidity Enzyme Immuno-Assay (EIA) and monitor changes in HIV incidence.

Discussion
Ending the HIV/AIDS pandemic by 2030 requires the continual monitoring and evaluation of prevention programmes, with the aim of optimising efforts and ensuring the achievement of epidemic control. This study will determine the impact DREAMS interventions have had on HIV incidence among AGYW in a ‘real world, non-trial setting’.