bluuebunny/crossref_metadata_2025_split huggingface dataset:
A resource database for protein kinase substrate sequence-preference motifs based on large-scale mass spectrometry data
Authors: Poll Brian G. , Leo Kirby T. , Deshpande Venky , Jayatissa Nipun , Pisitkun Trairak , Park Euijung , Yang Chin-Rang , Raghuram Viswanathan , Knepper Mark A. 
Published: February 2024

Abstract
Background
Protein phosphorylation is one of the most prevalent posttranslational modifications involved in molecular control of cellular processes, and is mediated by over 520 protein kinases in humans and other mammals. Identification of the protein kinases responsible for phosphorylation events is key to understanding signaling pathways. Unbiased phosphoproteomics experiments have generated a wealth of data that can be used to identify protein kinase targets and their preferred substrate sequences.

Methods
This study utilized prior data from mass spectrometry-based studies identifying sites of protein phosphorylation after in vitro incubation of protein mixtures with recombinant protein kinases. PTM-Logo software was used with these data to generate position-dependent Shannon information matrices and sequence motif ‘logos’. Webpages were constructed for facile access to logos for each kinase and a new stand-alone application was written in Python that uses the position-dependent Shannon information matrices to identify kinases most likely to phosphorylate a particular phosphorylation site.

Results
A database of kinase substrate target preference logos allows browsing, searching, or downloading target motif data for each protein kinase (https://esbl.nhlbi.nih.gov/Databases/Kinase_Logos/). These logos were combined with phylogenetic analysis of protein kinase catalytic sequences to reveal substrate preference patterns specific to particular groups of kinases (https://esbl.nhlbi.nih.gov/Databases/Kinase_Logos/KinaseTree.html). A stand-alone program, KinasePredictor, is provided (https://esbl.nhlbi.nih.gov/Databases/Kinase_Logos/KinasePredictor.html). It takes as input, amino-acid sequences surrounding a given phosphorylation site and generates a ranked list of protein kinases most likely to phosphorylate that site.

Conclusions
This study provides three new resources for protein kinase characterization. It provides a tool for prediction of kinase-substrate interactions, which in combination with other types of data (co-localization, etc.), can predict which kinases are likely responsible for a given phosphorylation event in a given tissue.
Effects of transcranial direct current stimulation alone and in combination with rehabilitation therapies on gait and balance among individuals with Parkinson’s disease: a systematic review and meta-analysis
Authors: Nguyen Thi Xuan Dieu , Mai Phuc Thi , Chang Ya-Ju , Hsieh Tsung-Hsun 
Published: February 2024

Abstract
Background
Parkinson’s disease (PD) is a neurogenerative disorder implicated in dysfunctions of motor functions, particularly gait and balance. Transcranial direct current stimulation (tDCS) is a noninvasive brain stimulation offered as a potential adjuvant therapy for PD. This systematic review and meta-analysis were conducted to identify whether tDCS alone and combined with additional rehabilitation therapies improve gait and balance among individuals with PD.

Methods
We searched PubMed, Embase, Web of Science, and relevant databases for eligible studies from inception to December 2022. Studies with a comparative design investigating the effects of tDCS on motor functions, including gait and balance among individuals with PD, were included. A meta-analysis was performed for each outcome using a random effects model for subgroup analysis and pooling of overall effect sizes.

Results
A total of 23 studies were included in the meta-analysis. The pooled results revealed that tDCS has moderate overall effects on gait, measured by gait speed (standardized mean deviation [SMD] = 0.238; 95% confidence interval [CI]  − 0.026 to 0.502); stride length (SMD = 0.318; 95% CI − 0.015 to 0.652); cadence (SMD =  − 0.632; 95% CI − 0.932 to − 0.333); freezing of gait questionnaire scores (SMD =  − 0.360; 95% CI − 0.692 to − 0.027); step length (SMD = 0.459; 95% CI − 0.031 to 0.949); walking time (SMD =  − 0.253; 95% CI − 0.758 to 0.252); stride time (SMD =  − 0.785; 95% CI: − 1.680 to 0.111); double support time (SMD = 1.139; 95% CI − 0.244 to 0.523); and balance, measured by timed up and go (TUG) test (SMD =  − 0.294; 95% CI − 0.516 to − 0.073), Berg balance scale (BBS) scores (SMD = 0.406; 95% CI − 0.059 to 0.87), and dynamic gait index (SMD = 0.275; 95% CI − 0.349 to 0.898). For the subgroup analysis, gait and balance demonstrated moderate effect sizes. However, only cadence, stride time, and TUG indicated a significant difference between real and sham tDCS (P = 0.027, P = 0.002, and P = 0.023, respectively), whereas cadence and BBS (P < 0.01 and P = 0.045, respectively) significantly differed after real tDCS plus other therapies rather than after sham tDCS plus other therapies.

Conclusions
Our results indicated that tDCS is significantly associated with gait and balance improvements among individuals with PD. The findings of this study provide more proof supporting the effectiveness of tDCS, encouraging tDCS to be utilized alone or in combination with other therapies in clinical practice for PD rehabilitation.
Pull me – push you? The disparate financing mechanisms of drug research in global health
Authors: Matthey Max Alexander , Hollis Aidan 
Published: February 2024

Abstract
Background
There is an inconsistency in the way pharmaceutical research is financed. While pull mechanisms are predominantly used to incentivize later-stage pharmaceutical research for products with demand in the Global North, so-called neglected diseases are chiefly financed by push funding. This discrepancy has so far been ignored in the academic debate, and any compelling explanation for why we draw the line between push and pull at poor people is lacking.

Main body
Clinical development of new pharmaceuticals is chiefly financed by free market pull mechanisms. Even in cases where markets fail to deliver adequate incentives, demand enhancement mechanisms are used to replicate pull funding artificially, for example, with subscription models for antibiotics. Push funding in clinical research is almost always used when the poverty of patients means that markets fail to create sufficient demand. The general question of whether push or pull generally is the more efficient way to conduct pharmaceutical research arises.

Conclusions
If the state is efficient in directing limited budgets for pharmaceutical research, push funding should be expanded to global diseases. If private industry is the more efficient actor, there would be enormous value in experimenting more aggressively with different approaches to enhance market demand artificially for neglected diseases.
Plant use and perceptions in the context of sexual health among people of Congolese descent in Belgium
Authors: Van Damme Laura , Chatrou Lars , de la Peña Eduardo , Kibungu Pathy , Bolya Césarine Sinatu , Van Damme Patrick , Vanhove Wouter , Ceuterick Melissa , De Meyer Emiel 
Published: February 2024

Abstract
Background
The use of medicinal plants is integral to global healthcare systems, with Sub-Saharan Africa maintaining a robust tradition of herbal medicine alongside Western-oriented healthcare. As migrant communities tend to continue traditional herbal practices after migration, documenting this use is vital to develop culturally sensitive healthcare. This study investigates plant usage and perspectives in the context of sexual and reproductive health among the Congolese community in Belgium, particularly in the Matongé quarter of Brussels. Our research questions were: (1) What is the current knowledge of medicinal plants among the Congolese community in Belgium in the context of sexual health, and what are the applications and commonly employed administration methods of these plants? (2) What role does herbal medicine play in the context of sexual health for people of Congolese descent in Belgium and how this is influenced by perceptions of sexuality? and (3) Is there a gender bias in the use of medicinal plants, and if so, can this be related to perceived gender norms?

Methods
We conducted 22 semi-structured interviews with people of Congolese descent currently living in Belgium. Participants were selected using both snowball sampling and purposive sampling. Plant use in the context of sexual health was recorded through freelisting. Data on narratives, ideas, and perceptions of this plant use in the context of sexual health were collected. Interview transcripts were analyzed using thematic analysis.

Results
We identified 17 plant species used for sexual health. Three overarching themes emerged from our data. Plants were used with a notable gender bias favoring male sexual potency enhancement. Men used these plants for both remedying potency issues and enhancing sexual prowess. In contrast, knowledge about plants for female sexual health was limited. Gender norms reinforced the importance of male sexual potency, while stigmatizing open discussions of female sexuality.

Conclusions
The use of medicinal plants for sexual health raises health, social, and conservation concerns, underscoring the need for further research in this area. This study contributes to understanding medicinal plant use within the Congolese community in Belgium and highlights the necessity for future research on herbal practices for female sexual health in this context.
Laid-back breastfeeding: knowledge, attitudes and practices of midwives and student midwives in Ireland
Authors: McGuigan Margaret , Larkin Patricia 
Published: February 2024

Abstract
Background
Despite concerted efforts by policy developers, health professionals and lay groups, breastfeeding rates in Ireland remain one of the lowest in world, with 63.6% of mothers initiating breastfeeding at birth, dropping to 37.6% of mothers breastfeeding exclusively on hospital discharge. Nipple trauma and difficulties with baby latching are major contributors to the introduction of formula and discontinuation of breastfeeding. Research shows laid-back breastfeeding (LBBF) significantly reduces breast problems such as sore and cracked nipples, engorgement, and mastitis as well as facilitating a better latch. Although the benefits of LBBF are well documented, this position does not seem to be routinely suggested to mothers as an option when establishing breastfeeding. This study aims to determine midwives’ and student midwives’ knowledge, attitudes, and practices of using laid-back breastfeeding in Ireland.

Method
A cross-sectional descriptive survey distributed to midwives and student midwives in three maternity hospitals in Ireland and two online midwifery groups based in the Republic of Ireland, during June, July, and August 2021.

Results
Two hundred and fifty-three valid responses were received from nine maternity units. Most participants (81.4%) were aware of laid-back breastfeeding. However, only 6.8% of respondents cited it as the position they most frequently use. Over one-third (38.34%) had never used this position with mothers. Those more likely to suggest LBBF had personal experience of it, were lactation consultants or working towards qualification, or had participated in specific education about LBBF. Barriers included lack of education, confidence, time, and experience. Further issues related to work culture, a tendency to continue using more familiar positions and concerns about mothers’ anatomy and mothers’ unfamiliarity with LBBF.

Conclusion
Although there was a high level of awareness of laid-back breastfeeding among midwives and student midwives, there are challenges preventing its use in practice. Education specifically related to using LBBF in practice is required to overcome the barriers identified. A greater understanding of mothers’ and babies’ intrinsic feeding capacities may give midwives more confidence to recommend this method as a first choice, potentially leading to more successful breastfeeding establishment and maintenance.
Sustaining the collaborative chronic care model in outpatient mental health: a matrixed multiple case study
Authors: Kim Bo , Sullivan Jennifer L. , Brown Madisen E. , Connolly Samantha L. , Spitzer Elizabeth G. , Bailey Hannah M. , Sippel Lauren M. , Weaver Kendra , Miller Christopher J. 
Published: February 2024

AbstractBackgroundSustaining evidence-based practices (EBPs) is crucial to ensuring care quality and addressing health disparities. Approaches to identifying factors related to sustainability are critically needed. One such approach is Matrixed Multiple Case Study (MMCS), which identifies factors and their combinations that influence implementation. We applied MMCS to identify factors related to the sustainability of the evidence-based Collaborative Chronic Care Model (CCM) at nine Department of Veterans Affairs (VA) outpatient mental health clinics, 3–4 years after implementation support had concluded.MethodsWe conducted a directed content analysis of 30 provider interviews, using 6 CCM elements and 4 Integrated Promoting Action on Research Implementation in Health Services (i-PARIHS) domains as codes. Based on CCM code summaries, we designated each site as high/medium/low sustainability. We used i-PARIHS code summaries to identify relevant factors for each site, the extent of their presence, and the type of influence they had on sustainability (enabling/neutral/hindering/unclear). We organized these data into a sortable matrix and assessed sustainability-related cross-site trends.ResultsCCM sustainability status was distributed among the sites, with three sites each being high, medium, and low. Twenty-five factors were identified from the i-PARIHS code summaries, of which 3 exhibited strong trends by sustainability status (relevant i-PARIHS domain in square brackets): “Collaborativeness/Teamwork [Recipients],” “Staff/Leadership turnover [Recipients],” and “Having a consistent/strong internal facilitator [Facilitation]” during and after active implementation. At most high-sustainability sites only, (i) “Having a knowledgeable/helpful external facilitator [Facilitation]” was variably present and enabled sustainability when present, while (ii) “Clarity about what CCM comprises [Innovation],” “Interdisciplinary coordination [Recipients],” and “Adequate clinic space for CCM team members [Context]” were somewhat or less present with mixed influences on sustainability.ConclusionsMMCS revealed that CCM sustainability in VA outpatient mental health clinics may be related most strongly to provider collaboration, knowledge retention during staff/leadership transitions, and availability of skilled internal facilitators. These findings have informed a subsequent CCM implementation trial that prospectively examines whether enhancing the above-mentioned factors within implementation facilitation improves sustainability. MMCS is a systematic approach to multi-site examination that can be used to investigate sustainability-related factors applicable to other EBPs and across multiple contexts.
Intrapulmonary migration of a fractured acupuncture needle: a case report
Authors: Liu Lei , Ma Dong-Jie , Qin Ying-Zhi , Liu Hongsheng 
Published: February 2024

Abstract
Background
Acupuncture, a traditional Chinese medical treatment, has been gaining popularity over the years. However, it also presents certain risks. We report a case of a patient who discovered a foreign body in their lung several years after undergoing acupuncture.

Case presentation
A middle-aged woman presented to our hospital with chest pain. An X-ray revealed a needle-like foreign body in the middle lobe of her right lung. The patient had previously undergone acupuncture treatment for local pain in her lower back and lower extremities many years prior. Based on the imaging findings and her medical history, we hypothesized that the foreign body in her lung was a result of a dislodged acupuncture needle. Through preoperative 3-dimensional reconstruction and indocyanine green localization, we were able to locate the foreign body in the lateral segment of the right middle lobe. We successfully removed the foreign body via wedge resection, and the patient made a smooth recovery post-surgery.

Conclusion
Acupuncturists and surgeons should remain vigilant about the potential risks associated with acupuncture.
RegistrAME: the Spanish self-reported patient registry of spinal muscular atrophy
Authors: Cattinari Maria Grazia , de Lemus Mencía , Tizzano Eduardo 
Published: February 2024

Abstract
Background
Spinal Muscular Atrophy (SMA) is a rare neuromuscular disorder characterized by progressive degeneration of motor neurons and muscle weakness resulting in premature death or severe motor disability. Over the last decade, SMA has dramatically changed thanks to new advances in care and the emergence of disease-specific treatments. RegistrAME is a self-reported specific disease registry with an accurate curation system. It has collected data on SMA patients in Spain since 2015, gathering demographic, clinical, and patient-reported outcome data, all of which are patient-relevant. RegistrAME is part of the TREAT NMD network. This study aims to describe the advantages and disadvantages of a self–reported SMA registry, as well as the different variables of interest in the health status of RegistrAME patients.

Results
In total, 295 living patients with a confirmed diagnosis of SMA-5q were included (aged 1 to 77 years; mean 20.28). Half of the patients (50.2%) were ≥ 16 years old; 22.03% were type 1, 48.47% were type 2, 28.82% were type 3, and 0.7% were type 4. All functional statuses (non-sitter, sitter, and walkers) could be observed in each SMA type. Adult patients harbored the least aggressive SMA types, however, they presented the greatest level of disability. Patients with SMA type 1 had scoliosis surgery about five years earlier than patients with SMA type 2. None of the type 1 patients who achieved ambulation were wheelchair-free outdoors. This was also evident in 62.5% of type 2 walker patients and 44% of type 3 walker patients. Of the SMA type 1 patients, 40% had a gastrostomy (of which 84% had two SMN2 copies). One in five children with SMA type 1 (one to seven years of age) were ventilation-free.

Conclusions
The information provided by RegistrAME in a “real-world” setting allows better management of family expectations, an adequate approach to the disease and patients’ needs, as well as a better understanding of the impact of the disease. It also helps monitor the evolution of care, which will result in the need for updated guidelines.
Factors affecting overall care experience for people living with rare conditions in the UK: exploratory analysis of a quantitative patient experience survey
Authors: Jones Jennifer , Cruddas Marie , Simpson Amy , Meade Nick , Pushparajah Daphnee , Peter Michelle , Hunter Amy 
Published: February 2024

Abstract
Background
Although individually rare, collectively, rare conditions are common and affect a large number of people and are often chronic, life threatening and affect multiple body systems; the majority of them have no effective treatment. The literature has identified many specific challenges for those living with rare conditions, however, we do not know which of these in combination are most likely to impact how someone rates their overall experience of care. The aim of this study is to do further exploratory analysis of the Genetic Alliance UK 2020 Rare Experience survey data to identify which variables are most strongly associated with respondents’ overall care experience.

Results
There were strong associations between most of the selected survey variables and the overall rated experience of care variable. In the multiple linear regression only nine variables remained in the best fit model: ‘Trust and confidence in hospital staff involved in ongoing care’; ‘Satisfaction with information provided by healthcare professionals—following diagnosis’; ‘The professionals providing care work as a team’; ‘Feel care is coordinated effectively’; ‘The timing and frequency of appointments are convenient for the patient/carer/family’; ‘Whether or not there is a specific healthcare professional to ask questions of about the rare/undiagnosed condition’; ‘Experience of searching for a diagnosis’; ‘Knowledge of whether there is a specialist centre for the condition’; and ‘Number of different clinics attend for the condition’.

Conclusions
Our findings indicate the challenges that play the largest part in explaining the varied experiences with rare disease healthcare in the UK for our survey respondents. These challenges should be further investigated with a broader sample of people affected by rare conditions, ideally through the implementation of a comprehensive national rare condition patient registry. Our findings highlight an important potential gap in the Framework, ‘trust and confidence in healthcare professionals’; further research is required to fully understand the foundations of trust and confidence.
Ultrasound radiomics signature for predicting central lymph node metastasis in clinically node-negative papillary thyroid microcarcinoma
Authors: Liu Jie , Yu Jingchao , Wei Yanan , Li Wei , Lu Jinle , Chen Yating , Wang Meng 
Published: February 2024

Abstract
Background
Whether prophylactic central lymph node dissection is necessary for patients with clinically node-negative (cN0) papillary thyroid microcarcinoma (PTMC) remains controversial. Herein, we aimed to establish an ultrasound (US) radiomics (Rad) score for assessing the probability of central lymph node metastasis (CLNM) in such patients.

Methods
480 patients (327 in the training cohort, 153 in the validation cohort) who underwent thyroid surgery for cN0 PTMC at two institutions between January 2018 and December 2020 were included. Radiomics features were extracted from the US images. Least absolute shrinkage and selection operator logistic regression were utilized to generate a Rad score. A nomogram consisting of the Rad score and clinical factors was then constructed for the training cohort. Both cohorts assessed model performance using discrimination, calibration, and clinical usefulness.

Results
Based on the six most valuable radiomics features, the Rad score was calculated for each patient. A multivariate analysis revealed that a higher Rad score (P < 0.001), younger age (P = 0.006), and presence of capsule invasion (P = 0.030) were independently associated with CLNM. A nomogram integrating these three factors demonstrated good calibration and promising clinical utility in the training and validation cohorts. The nomogram yielded areas under the curve of 0.795 (95% confidence interval [CI], 0.745–0.846) and 0.774 (95% CI, 0.696–0.852) in the training and validation cohorts, respectively.

Conclusions
The radiomics nomogram may be a clinically useful tool for the individual prediction of CLNM in patients with cN0 PTMC.