bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracorporeal shock wave lithotripsy as monotherapy for vesical calculi
Authors: Nagaraj Arjun , Madineni Bhavana Chowdary , Harohally Krishnareddy Nagaraj , Nagaraj Jeevan , Iqbal Tariq , Kamble Nitin Kumar , Varghese Jofin John 
Published: January 2024

Abstract
Background
Extracorporeal shock wave lithotripsy (ESWL) is a well-established non-surgical treatment of urolithiasis. ESWL as a monotherapy to treat vesical calculi is still unfamiliar among many urologists, despite its early introduction in the 1990’s. ESWL monotherapy for vesical calculi was performed in our study in a unique fashion in supine position with full bladder unlike any other previous reported studies.

Methods
We aimed this study to report our experience with ESWL as a monotherapy in treating urinary bladder stones with a unique technique. A total of 29 patients with vesical calculi were treated with ESWL monotherapy from May 2021 to January 2023 using Dornier delta lithotripter in the supine position with the full bladder without per urethral catheterisation. Patients with stone size > 2.5cm or Hounsfield units > 1200 were excluded. Stone clearance was assessed with the help of fluoroscopy and ultrasonography on a second visit on day 7 after the procedure. Patients were followed up for 3 months.

Results
The mean size of vesical calculus was 1.6 cm (SD 0.32), and the mean Hounsfield unit was 940 HU (SD 86.61). None of the study subjects required surgical intervention. The stone clearance was obtained in 93.1% after a single session. The remaining two patients (6.9%) required one more session of ESWL following which stone clearance was obtained. One patient had acute urinary retention, and five (17.2%) patients had mild haematuria.

Conclusion
ESWL monotherapy is a safe and effective treatment option for vesical calculi, with minimal or no patient discomfort, when done in supine position without routine per urethral catheterisation as described in the study. It should be considered more often by practicing urologists for vesical calculi.
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots
Authors: Carter Clayton , Saporito Aaron , Douglass Stephen M. 
Published: January 2024

Abstract
Background
Metagene plots provide a visualization of biological signal trends over subsections of the genome and are used to perform high-level analysis of experimental data by aggregating genome-level data to create an average profile. The generation of metagene plots is useful for summarizing the results of many sequencing-based applications. Despite their prevalence and utility, the standard metagene plot is blind to conflicting signals within data. If multiple distinct trends occur, they can interact destructively, creating a plot that does not accurately represent any of the underlying trends.

Results
We present MetageneCluster, a Python tool to generate a collection of representative metagene plots based on k-means clustering of genomic regions of interest. Clustering the data by similarity allows us to identify patterns within the features of interest. We are then able to summarize each pattern present in the data, rather than averaging across the entire feature space. We show that our method performs well when used to identify conflicting signals in real-world genome-level data.

Conclusions
Overall, MetageneCluster is a user-friendly tool for the creation of metagene plots that capture distinct patterns in underlying sequence data.
MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis
Authors: Steinke Kat , Pamp Sünje J. , Munk Patrick 
Published: January 2024

Abstract
Background
The possibility of recovering metagenome-assembled genomes (MAGs) from sequence reads allows for further insights into microbial communities and their members, possibly even analyzing such sequences with tools designed for single-isolate genomes. As result quality depends on sequence quality, performance of tools for single-isolate genomes on MAGs should be tested beforehand. Bioinformatics can be leveraged to quickly create varied synthetic test sets with known composition for this purpose.

Results
We present MAGICIAN, a flexible, user-friendly pipeline for the simulation of MAGs. MAGICIAN combines a synthetic metagenome simulator with a metagenomic assembly and binning pipeline to simulate MAGs based on user-supplied input genomes, allowing users to test performance of tools on MAGs while having a ground truth to compare results to. Using MAGICIAN, we found that even very slight (1%) changes in depth of coverage can drastically affect whether a genome can be recovered. We also demonstrate the use of simulated MAGs by evaluating the suitability of such genomes obtained with MAGICIAN’s current default pipeline for analysis with the antimicrobial resistance gene identification tool ResFinder.

Conclusions
Using MAGICIAN, it is possible to simulate MAGs which, while generally high in quality, reflect issues encountered with real-world data, thus providing realistic best-case data. Evaluating the results of ResFinder analysis of these genomes revealed a risk for plausible-looking false positives, which underlines the need for pipeline validation so that researchers are aware of the potential issues when interpreting real-world data. Furthermore, the effects of fluctuations in depth of coverage on genome recovery in our simulated “random sequencing” warrant further investigation and indicate random subsampling of reads may affect discovery of more genomes.
Supraglottic jet oxygenation and ventilation improves oxygenation during endoscopic retrograde cholangiopancreatography: a randomized controlled clinical trial
Authors: Su Dan , Zhang Wei , Li Jingze , Tan Xi , Wei Huafeng , Wang Yinglin , Ji Zhonghua 
Published: January 2024

Abstract
Purpose
Hypoxia is one of the most frequent adverse events under deep sedation in the semiprone position. We hypothesized that supraglottic jet oxygenation and ventilation (SJOV) via Wei nasal jet tube (WNJ) can reduce the incidence of hypoxia in patients under deep sedation during endoscopic retrograde cholangiopancreatography (ERCP).

Methods
A total of 171 patients were divided into three groups: N group, supplementary oxygen via a nasopharyngeal airway (4–6 L/min); W group, supplementary oxygen via WNJ (4–6 L/min); WS group, SJOV via WNJ. The primary outcome was the incidence of adverse events, including sedation-related adverse events [SRAEs, hypoxemia (SpO2 = 75–89% lasted less than 60 s); severe hypoxemia (SpO2 < 75% at any time or SpO2 < 90% lasted more than 60 s] and subclinical respiratory depression (SpO2 = 90–95%). Other intraoperative and post-operative adverse events were also recorded as secondary outcomes.

Results
Compared with the N group, the incidence of hypoxemia and subclinical respiratory depression in the WS group was significantly lower (21% vs. 4%, P = 0.005; 27% vs. 6%, P = 0.002). Compared with Group W, the incidence of hypoxemia and subclinical respiratory depression in Group WS was also significantly less frequent (20% vs. 4%, P = 0.009; 21% vs. 6%, P = 0.014). No severe hypoxia occurred in the group WS, while four and one instances were observed in the group N and group W respectively. There were no significant differences in other adverse events among the three groups.

Conclusion
SJOV can effectively improve oxygenation during ERCP in deeply sedated semiprone patients.
The impact of diet quality on cognitive ability of Chinese older adults: evidence from the China Health and Nutrition Survey (CHNS)
Authors: Xu Ziwei , Chen Shuaizhen , Guo Min , Zhang Tianlei , Niu Xiaoxuan , Zhou Yuxin , Tan Jialong , Wang Jian 
Published: January 2024

Abstract
Background
Numerous studies have demonstrated a positive correlation between diet quality and cognitive performance, indicating that improving diet quality may be beneficial in preventing cognitive decline in older adults. However, few study has investigated the causal relationship between diet quality and cognitive performance. The purpose of this study is to evaluate the causal effects of diet quality on cognitive performance in Chinese adults aged 55 years and older. Particularly, we utilize the Chinese Diet Quality Index (CHEI), a dietary assessment tool tailored for Chinese populations, as a proxy for older adults’ diet quality.

Methods
Data were obtained from the China Health and Nutrition Survey (CHNS) ($$N = 2337$$

N
=
2337

, $$\ge$$
≥
55 years old) conducted in 2004 and 2006. Cognitive function was tested by a subset of items from the Telephone Interview for Cognitive Status-Modified (TICS-m). Data on dietary intake was retrieved from three consecutive 24 hour recalls by participants and its quality was assessed by the 17-items Chinese Healthy Eating Index (CHEI). An Instrumental Variable technique was used to deal with the potential endogeneity of dietary quality. The instrumental variable used in our study is the community mean of CHEI.

Results
After adjusting for socio-demographic factors (age, gender, education, per capita household income), lifestyle habits (smoking, alcohol consumption, physical activity, BMI), and chronic diseases (hypertension, diabetes), our findings revealed that improving diet quality had a significant positive effect on cognitive performance ($$P = 0.020$$

P
=
0.020

), particularly in females aged 55-65 years ($$P = 0.003$$

P
=
0.003

) and females with primary education and below ($$P < 0.001$$

P
<
0.001

).

Conclusion
Our study suggests that improving diet quality and adhering to the Dietary Guidelines for Chinese may enhance cognitive performance in Chinese adults aged 55 years and older.
Perspectives of telemedicine-based services among family caregivers of patients with end-of-life cancer: a qualitative study in mainland China
Authors: Guo Junchen , Xu Xianghua , Liu Chaoyi , Wang Ying , Chen Yongyi 
Published: January 2024

Abstract
Background
Despite being driven by a strong sense of duty and familial obligation, providing care for patients nearing the end of life poses challenges for family caregivers. Telemedicine has rapidly gained traction as a transformative approach to healthcare delivery, offering an array of benefits that could be particularly valuable in end-of-life care. However, research on the perspectives of telemedicine-based services among family caregivers of patients with end-of-life cancer is limited. Therefore, this study aims to explore the perspectives and preferences of telemedicine-based services among family caregivers of patients with end-of-life cancer and provide a framework for developing and executing a tailored telemedicine-based end-of-life care program that addresses the unique needs of family caregivers in mainland China.

Method
A descriptive phenomenological approach was used. Family caregivers were selected using purposive sampling at a tertiary cancer hospital. One-on-one semi-structured interviews were conducted with the participants from November to December 2022. Colaizz’s method was used to analyze the interviews.

Results
Fourteen participants participated in interviews. Three themes and ten subthemes were identified: motivation to receive telemedicine services (relief from the burden of home care; access to professional health care services), supportive care needs for telemedicine services (support for symptom management; negative emotional adjustment; death education; daily life care guidance), and functional expectations of telemedicine service platforms (ease of use; real-time online guidance and response; personalized automatic reminder; targeted matching push of health knowledge).

Conclusion
Family caregivers expressed interest in telemedicine-based services and identified various care needs before receiving telemedicine services. The findings of this study can help policymakers and healthcare providers develop more effective and culturally appropriate telemedicine-based service programs that can better support family caregivers of end-of-life cancer patients.
Definition and validation of the nursing diagnosis label “wish to die”: a research protocol
Authors: Monforte-Royo Cristina , Goni-Fuste Blanca , Crespo Iris , Pergolizzi Denise , Martin-Delgado Leandra , Fuster Pilar , Bellido-Perez Mercedes , Tomás-Sábado Joaquín , Rodríguez-Prat Andrea 
Published: January 2024

Abstract
Background
Euthanasia has been incorporated into the health services of seven countries. The legalisation of these practices has important repercussions for the competences of nurses, and it raises questions about their role. When a patient with advanced disease expresses a wish to die, what is expected of nurses? What are the needs of these patients, and what kind of care plan do they require? What level of autonomy might nurses have when caring for these patients? The degree of autonomy that nurses might or should have when it comes to addressing such a wish and caring for these patients has yet to be defined. Recognising the wish to die as a nursing diagnosis would be an important step towards ensuring that these patients receive adequate nursing care.
This study-protocol aims to define and validate the nursing diagnosis wish to die in patients with advanced disease, establishing its defining characteristics and related factors; to define nursing-specific interventions for this new diagnosis.

Methods
A prospective three-phase study will be carried out. Phase-A) Foundational knowledge: an umbrella review of systematic reviews will be conducted; Phase-B) Definition and validation of the diagnostic nomenclature, defining characteristics and related factors by means of an expert panel, a Delphi study and application of Fehring’s diagnostic content validation model; Phase-C) Definition of nursing-specific interventions for the new diagnosis. At least 200 academic and clinical nurses with expertise in the field of palliative care or primary health care will be recruited as participants across the three phases.

Discussion
The definition of the wish to die as a nursing diagnosis would promote greater recognition and autonomy for nurses in the care of patients who express such a wish, providing an opportunity to alleviate underlying suffering through nursing-specific interventions and drawing attention to the needs of patients with advanced disease. The new diagnosis would be an addition to nursing science and would provide a framework for providing care to people with advanced disease who express such a wish. Nurses would gain professional autonomy about identifying, exploring and responding clinically to such a wish.
Immune evasion in cell-based immunotherapy: unraveling challenges and novel strategies
Authors: Li Yan-Ruide , Halladay Tyler , Yang Lili 
Published: January 2024

AbstractCell-based immunotherapies (CBIs), notably exemplified by chimeric antigen receptor (CAR)-engineered T (CAR-T) cell therapy, have emerged as groundbreaking approaches for cancer therapy. Nevertheless, akin to various other therapeutic modalities, tumor cells employ counterstrategies to manifest immune evasion, thereby circumventing the impact of CBIs. This phenomenon is facilitated by an intricately immunosuppression entrenched within the tumor microenvironment (TME). Principal mechanisms underpinning tumor immune evasion from CBIs encompass loss of antigens, downregulation of antigen presentation, activation of immune checkpoint pathways, initiation of anti-apoptotic cascades, and induction of immune dysfunction and exhaustion. In this review, we delve into the intrinsic mechanisms underlying the capacity of tumor cells to resist CBIs and proffer prospective stratagems to navigate around these challenges.
Phenotypic resistance not associated with knockdown mutations (kdr) in Anopheles albimanus exposed to deltamethrin in southern coastal Ecuador
Authors: Real-Jaramillo Sebasthian , Bustillos Juan J. , Moncayo Ana L. , Neira Marco , Fárez Leonardo , Beltrán Efraín , Ocaña-Mayorga Sofía 
Published: January 2024

Abstract
Background
Decrease in malaria rates (e.g. incidence and cases) in Latin America maintains this region on track to achieve the goal of elimination. During the last 5 years, three countries have been certified as malaria free. However, the region fails to achieve the goal of 40% reduction on malaria rates and an increase of cases has been reported in some countries, including Ecuador. This scenario has been associated with multiple causes, such as decrease of funding to continue anti-malarial programmes and the development of insecticide resistance of the main malaria vectors. In Ecuador, official reports indicated phenotypic resistance in Aedes aegypti and Anopheles albimanus to deltamethrin and malathion, particularly in the coastal areas of Ecuador, however, information about the mechanisms of resistance have not been yet elucidated. This study aims to evaluate phenotypic response to deltamethrin and its relationship with kdr mutations in An. albimanus from two localities with different agricultural activities in southern coastal Ecuador.

Methods
The CDC bottle assay was carried out to evaluate the phenotypic status of the mosquito’s population. Sequencing the voltage gated sodium channel gene (VGSC) sought knockdown mutations (kdr) in codons 1010, 1013 and 1014 associated with resistance.

Results
Phenotypic resistance was found in Santa Rosa (63.3%) and suspected resistance in Huaquillas (82.1%); with females presenting a higher median of knockdown rate (83.7%) than males (45.6%). No statistical differences were found between the distributions of knockdown rate for the two localities (p = 0.6048) which indicates no influence of agricultural activity. Although phenotypic resistance was confirmed, genetic analysis demonstrate that this resistance was not related with the kdr mechanism of the VGSC gene because no mutations were found in codons 1010 and 1013, while in codon 1014, 90.6% showed the susceptible sequence (TTG) and 7.3% ambiguous nucleotides (TKK and TYG).

Conclusions
These results highlighted the importance of continuous monitoring of resistance in malaria vectors in Ecuador, particularly in areas that have reported outbreaks during the last years. It is also important to elucidate the mechanism involved in the development of the resistance to PYs to propose alternative insecticides or strategies for vector control in areas where resistance is present.
Whoever wants better healthcare simply pays more: citizens' perception about voluntary private health insurance in Colombia
Authors: Patiño-Lugo Daniel Felipe , Vélez Claudia Marcela , Díaz-Hernández Diana Patricia , Salazar-Blanco Olga Francisca , González-Arango Juan Esteban , Velásquez-Correa Juan Carlos , Rodríguez-Corredor Leydi Camila , Vélez-Marín Viviana María , Velásquez-Salazar Pamela 
Published: January 2024

Abstract
Objectives
To explore the perceptions that Colombians have about voluntary private health insurance plans (VPHI) in the health system to identify the tensions that exist between the public and private systems.

Methods
A qualitative case study approach with 46 semi structured interviews of patients, healthcare workers, healthcare administrators, decision-makers, and citizens. Interviews were recorded, transcribed, anonymized, digitally stored, and analyzed following grounded theory guidelines.

Results
We developed a paradigmatic matrix that explores how, in a context mediated by both the commodification of health and social stratification, perceptions about the failures in the public health system related to lack of timely care, extensive administrative procedures, and the search for privileged care led to positioning VPHI as a solution to these failures. The interviewees identified three consequences of using VPHI: first, the worsening of problems of timely access to care in the public system; second, higher costs for citizens translated into double payment for technologies and services to which they are entitled; third, the widening of inequity gaps in access to health services between people with similar needs but different payment capacities.

Conclusions
These findings can help decision makers to understand citizens´ perceptions about the implications that VPHI may have in worsening equity gaps in the Colombian health system. It also shows, how VPHI is perceived as a double payment for services covered within social security plans and suggests that the perceived lack of timely access to care in the public systems and the fear that citizens have for themselves or their family members when using suboptimal healthcare are important drivers to purchase these private insurances.
Haitian women in New York City use global food plants for women’s health
Authors: Vardeman Ella T. , Kennelly Edward J. , Vandebroek Ina 
Published: January 2024

Abstract
Background
Despite the availability of mainstream biomedical healthcare in New York City (NYC), community-based ethnomedicine practices remain a low-cost, culturally relevant treatment for many immigrants. Previous urban ethnobotany research in NYC has established that several Caribbean communities continue using medicinal plants for women’s health after immigration. This study sought to address to what extent: (1) NYC Haitian women continue using medicinal plants for women’s health after migration; (2) their plants and the conditions treated were similar to those identified in an earlier survey with NYC immigrants from the Dominican Republic.

Methods
Through an ethnobotanical survey, 100 Haitian women living in NYC and born in Haiti were interviewed about their knowledge of medicinal plants for women’s health conditions. Reported species were purchased based on local names in NYC Haitian stores and markets, vouchered, and identified.

Results
Nearly all Haitian women (97%) reported using medicinal plants while living in Haiti. Most Haitian women continued using medicinal plants after coming to the USA (83%). The 14% decrease, although significant (z = 3.3; p = 0.001), was mainly due to logistical difficulties with sourcing plants after recent immigration. Popular medicinal plant species reported were primarily global food plants, re-emphasizing the intertwined food-medicine relationship in Caribbean diasporas. Comparison with data from NYC Dominicans identified childbirth and puerperium, gynecological infections, and vaginal cleansing as priority Haitian women’s health concerns treated with plants.

Conclusion
Our findings support the global nature of Caribbean migrant plant pharmacopeia, predominantly centered around food plants and adapted to transnational urban settings. They underscore cultural diversity, dispelling the notion of one uniform traditional knowledge system labeled “Caribbean.” The importance of preventative medicine for women’s health, particularly the regular consumption of “healthy” foods or teas highlights the role food plants play in maintaining health without seeking treatment for a particular condition. Cross-cultural comparisons with other NYC Caribbean immigrants emphasize the importance of conducting ethnobotanical surveys to ground-truth plant use in the community. Such surveys can also identify culture-specific health priorities treated with these plants. Healthcare providers can leverage these insights to formulate culturally relevant and community-tailored healthcare strategies aligned with Haitian women’s health beliefs and needs.