bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physeal Sparing Medial Patellofemoral Ligament Reconstruction With Suture Anchor for Femoral Fixation of Graft
Authors: Tayne Samantha , Kim Billy I. , Lau Brian C. 
Published: November 2022

Background: Patellar instability is a common problem in the active pediatric population. Physeal sparing medial patellofemoral ligament (MPFL) reconstruction using a soft suture anchor for femoral graft fixation has the proposed advantages of diminishing volumetric bony removal from the epiphysis, increasing the margin of safety with respect to notch, trochlear, and/or physeal damage, as well as reducing the risk of thermal damage to the physis during socket reaming. Indications: MPFL reconstruction is indicated in patients with recurrent patellar instability with MPFL tear or attenuation on magnetic resonance imaging or failure of conservative treatment. Physeal sparing techniques are necessary in the pediatric population to prevent growth disturbance and deformities that can lead to significant long-term disability. Technique Description: The patient was placed in supine position. Following examination under anesthesia, diagnostic arthroscopy was performed to assess for patellofemoral chondral defects. The surgical technique required 6 steps: (1) medial patellar dissection, (2) patellar anchor placement with 1.8-mm suture anchors, (3) medial femoral dissection over Schottle’s point, (4) femoral anchor placement using 2.8-mm double loaded anchor, (5) allograft femoral fixation, and (6) allograft patellar fixation. After skin closure, examination under anesthesia was repeated. Results: The patient was weight-bearing as tolerated immediately after surgery, using a brace for the first 6 weeks. Rehabilitation progressed from regaining range of motion, strengthening of the operative extremity, and returning to sport activities. In the senior author’s experience using this technique, there have been no recurrent patellar dislocations and no evidence of growth disturbance or angulation. One patient did find that the graft was prominent over the femoral epicondyle and returned to the operating room for debulking at 9 months postoperatively. Discussion/Conclusion: In conclusion, we propose that physeal sparing MPFL reconstruction using soft anchors for patellar and femoral fixation offers a simple and safe technique with reproducible anatomic graft placement and favorable clinical outcomes. This technique is technically simple and can be easily learned by surgeons familiar with adult MPFL reconstruction techniques. The author(s) attests that consent has been obtained from any patient(s) appearing in this publication. If the individual may be identifiable, the author(s) has included a statement of release or other written form of approval from the patient(s) with this submission for publication.
Genetic basis and molecular profiling in myeloproliferative neoplasms
Authors: Luque Paz Damien , Kralovics Robert , Skoda Radek C. 
Published: November 2022

Abstract
BCR::ABL1-negative myeloproliferative neoplasms (MPNs) are clonal diseases originating from a single hematopoietic stem cell that cause excessive production of mature blood cells. The 3 subtypes, that is, polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), are diagnosed according to the World Health Organization (WHO) and international consensus classification (ICC) criteria. Acquired gain-of-function mutations in 1 of 3 disease driver genes (JAK2, CALR, and MPL) are the causative events that can alone initiate and promote MPN disease without requiring additional cooperating mutations. JAK2-p.V617F is present in &gt;95% of PV patients, and also in about half of the patients with ET or PMF. ET and PMF are also caused by mutations in CALR or MPL. In ∼10% of MPN patients, those referred to as being “triple negative,” none of the known driver gene mutations can be detected. The common theme between the 3 driver gene mutations and triple-negative MPN is that the Janus kinase–signal transducer and activator of transcription (JAK/STAT) signaling pathway is constitutively activated. We review the recent advances in our understanding of the early events after the acquisition of a driver gene mutation. The limiting factor that determines the frequency at which MPN disease develops with a long latency is not the acquisition of driver gene mutations, but rather the expansion of the clone. Factors that control the conversion from clonal hematopoiesis to MPN disease include inherited predisposition, presence of additional mutations, and inflammation. The full extent of knowledge of the mutational landscape in individual MPN patients is now increasingly being used to predict outcome and chose the optimal therapy.
Physicians’ experiences and perceived challenges working in an emergency setting in Bharatpur, Nepal: a qualitative study
Authors: Hansen Kristoffer Lund , Bratholm Åsmund , Pradhan Manohar , Mikkelsen Søren , Milling Louise 
Published: November 2022

Abstract
Background
Emergency medical care, including prehospital treatment, forms an important component of any healthcare system. Like most low-middle-income countries, Nepal has an emergency medical system that can be described as underdeveloped. Emergency physicians navigating this system may experience challenges or barriers in their treatment of patients. This study aimed to investigate physicians’ perspectives on emergency and prehospital patient management in a low-income country, Nepal, and to understand the challenges and barriers they perceive in emergency treatment including both the prehospital treatment and the immediate in-hospital treatment at the emergency department.

Methods
Using a qualitative study, eight semi-structured interviews with physicians working in a Nepalese emergency department were performed. The interviews were conducted between September and November 2021 and were audio-recorded and transcribed verbatim. Data were subsequently analyzed using the systematic text condensation method.

Results
Four main themes and associated sub-themes were identified: (1) patients’ sociocultural, educational, and financial factors (such as financial issues and financial inequality) and regional differences; (2) emergency department’s organization and resources concerning human and material resources, protocols, and guidelines; (3) problems with the emergency department (ED) service’s qualities and availability caused by an insufficient integration of the ED and the EMS, prehospital resources, and financial interests in the EMS; and (4) surrounding healthcare system’s impact on the ED where, especially, the levels of organized primary care, governmental responsibilities, and healthcare structure were addressed.

Conclusions
The physicians identified numerous regularly encountered challenges and barriers. These challenges stretched beyond the ED and into various aspects of society. The patients’ financial problems were described as the greatest problem, restricting the treatment due to a given patient’s inability or unwillingness to pay for the required procedures. The physicians were thus restricted in completing their duties to the desired levels. The low quality of prehospital care and a lack of education and awareness of common diseases and symptoms in a significant proportion of patients were identified by many participants as being significant issues. The aforementioned challenges or barriers directly resulted in patients arriving in critical conditions that could have been avoided if the disease were treated earlier.
Multiple instance neural networks based on sparse attention for cancer detection using T-cell receptor sequences
Authors: Kim Younghoon , Wang Tao , Xiong Danyi , Wang Xinlei , Park Seongoh 
Published: November 2022

AbstractEarly detection of cancers has been much explored due to its paramount importance in biomedical fields. Among different types of data used to answer this biological question, studies based on T cell receptors (TCRs) are under recent spotlight due to the growing appreciation of the roles of the host immunity system in tumor biology. However, the one-to-many correspondence between a patient and multiple TCR sequences hinders researchers from simply adopting classical statistical/machine learning methods. There were recent attempts to model this type of data in the context of multiple instance learning (MIL). Despite the novel application of MIL to cancer detection using TCR sequences and the demonstrated adequate performance in several tumor types, there is still room for improvement, especially for certain cancer types. Furthermore, explainable neural network models are not fully investigated for this application. In this article, we propose multiple instance neural networks based on sparse attention (MINN-SA) to enhance the performance in cancer detection and explainability. The sparse attention structure drops out uninformative instances in each bag, achieving both interpretability and better predictive performance in combination with the skip connection. Our experiments show that MINN-SA yields the highest area under the ROC curve scores on average measured across 10 different types of cancers, compared to existing MIL approaches. Moreover, we observe from the estimated attentions that MINN-SA can identify the TCRs that are specific for tumor antigens in the same T cell repertoire.
Phylogenomic analysis and development of molecular markers for the determination of twelve plum cultivars (Prunus, Rosaceae)
Authors: Xu Yicen , Fang Bo , Li Jingling , Wang Yuanwei , Liu Jingting , Liu Chang , Yu Jie 
Published: November 2022

Abstract
Background
Plums are one of the most important economic crops of the Rosaceae family and are produced all over the world. China has many local varieties, but the genomic information is limited for genetic studies. Here, we first sequenced, assembled, and analyzed the plastomes of twelve plum cultivars and developed molecular markers to distinguish them.

Results
The twelve plastomes of plum cultivars have a circular structure of 157,863–157,952 bp containing a large single-copy region (LSC) of 86,109–86,287 bp, a small copy region (SSC) of 18,927–19,031 bp, and two inverted repeats (IR) of 26,353–26,387 bp each. The plastomes of plum cultivars encode 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. We detected 50, 54, 54, 53, 53, 50, 54, 54, 54, 49, 50, 54 SSRs in the twelve analyzed varieties, respectively. For repeat sequences, we identified 553 tandem repeats, 204 direct repeats, and 270 palindromic repeats. We also analyzed the expansion/contraction of IR regions. The genes rpl22, rps19, rpl2, ycf1, ndhF, and the trnH span on or near the boundary of IR and single-copy regions. Phylogenetic analysis showed that the twelve cultivars were clustered with the P. salicina and P. domestica. We developed eight markers LZ01 to LZ08 based on whole plastomes and nuclear genes and validated them successfully with six repetitions.

Conclusions
The results obtained here could fill in the blanks of the plastomes of these twelve plum cultivars and provide a wider perspective based on the basis of the plastomes of Prunus to the molecular identification and phylogenetic construction accurately. The analysis from this study provides an important and valuable resource for studying the genetic basis for agronomic and adaptive differentiation of the Prunus species.
Distribution, inducibility, and characterisation of prophages in Latilactobacillus sakei
Authors: Ambros Conrad L. , Ehrmann Matthias A. 
Published: November 2022

Abstract
Background
Lactic acid bacteria (LAB) are used as starters in a wide variety of food fermentations. While the number of reports of phages infecting other LAB steadily increased over the years, information about phage associated with Latilactobacillus sakei, a frequently used meat starter, remains scarce.

Results
In this study, a predictive genomic analysis of 43 Latilactobacillus sakei genomes revealed the presence of 26 intact, eleven questionable and 52 incomplete prophage sequences across all analysed genomes with a range of one to five predicted prophage sequences per strain. Screening 24 sakei strains for inducible prophages by utilising UV light or mitomycin C, we identified seven lysogenic strains showing lysis after induction during subsequent growth monitoring.
Electron microscopic analysis revealed fully assembled virions in the purified lysates of four samples, thus confirming successful prophage induction. All virions featured icosahedral, isomeric heads and long, most likely non-contractile tails indicating siphoviruses. By performing phylogenetic analyses with various marker genes as well as full prophage sequences, we displayed a remarkably high diversity of prophages, that share a similar gene module organisation and six different chromosomal integration sites were identified. By sequencing viral DNA purified from lysates of Latilactobacillus sakei TMW 1.46, we demonstrate that simultaneous induction of multiple prophages is possible.

Conclusions
With this work, we not only provide data about the incidence of prophages harboured by the meat starter Latilactobacillus sakei, we also demonstrated their potential to impact growth of their host after induction, as well as forming seemingly fully assembled virions.
Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS
Authors: Esposito Salvatore , Taranto Francesca , Vitale Paolo , Ficco Donatella Bianca Maria , Colecchia Salvatore Antonio , Stevanato Piergiorgio , De Vita Pasquale 
Published: November 2022

Abstract
Background
Rapid reductions in emissions from fossil fuel burning are needed to curb global climate change. Biofuel production from crop residues can contribute to reducing the energy crisis and environmental deterioration. Wheat is a renewable source for biofuels owing to the low cost and high availability of its residues. Thus, identifying candidate genes controlling these traits is pivotal for efficient biofuel production. Here, six multi-locus genome-wide association (ML-GWAS) models were applied using 185 tetraploid wheat accessions to detect quantitative trait nucleotides (QTNs) for fifteen traits associated with biomass composition.

Results
Among the 470 QTNs, only 72 identified by at least two models were considered as reliable. Among these latter, 16 also showed a significant effect on the corresponding trait (p.value < 0.05). Candidate genes survey carried out within 4 Mb flanking the QTNs, revealed putative biological functions associated with lipid transfer and metabolism, cell wall modifications, cell cycle, and photosynthesis. Four genes encoded as Cellulose Synthase (CeSa), Anaphase promoting complex (APC/C), Glucoronoxylan 4-O Methyltransferase (GXM) and HYPONASTIC LEAVES1 (HYL1) might be responsible for an increase in cellulose, and natural and acid detergent fiber (NDF and ADF) content in tetraploid wheat. In addition, the SNP marker RFL_Contig3228_2154 associated with the variation in stem solidness (Q.Scsb-3B) was validated through two molecular methods (High resolution melting; HRM and RNase H2-dependent PCR; rhAMP).

Conclusions
The study provides new insights into the genetic basis of biomass composition traits on tetraploid wheat. The application of six ML-GWAS models on a panel of diverse wheat genotypes represents an efficient approach to dissect complex traits with low heritability such as wheat straw composition. The discovery of genes/genomic regions associated with biomass production and straw quality parameters is expected to accelerate the development of high-yielding wheat varieties useful for biofuel production.
Anxiety and depression symptoms, albuminuria and risk of acute myocardial infarction in the Norwegian HUNT cohort study
Authors: Gustad Lise Tuset , Myklebust Tor Åge , Bjerkeset Ottar , Williams Lana J. , Laugsand Lars Erik , Dalen Håvard , Berk Michael , Romundstad Solfrid 
Published: November 2022

Abstract
Background
Studies suggest increased risk for an outcome in people with joint exposures that share common causal pathways. The objective of this study was to determine the risk of incident acute myocardial infarction (AMI) following exposure to both albuminuria and/or anxiety and depression symptoms.

Methods
Participants who provided urine samples to the HUNT2 (1995–97) or HUNT3 (2007–2009) surveys were followed until the end of 2016. Albuminuria was measured by Albumin Creatine Ratio (ACR) and participants self-reported mood and anxiety symptoms on the Hospital Anxiety and Depression scale. We used Cox regression to estimate hazard ratios (HRs) for first incident AMI considering interaction between exposures and additive models to calculate the proportion of AMI that were attributable to the synergy of both exposures, adjusted for the Framingham variables.

Results
Eleven thousand fourteen participants free of previous AMI were eligible for participation, with 1234 incident AMIs occurred during a mean 13.7 years of follow-up. For participants who had a healthier CVD risk profile, the HR for AMI of having both albuminuria (3–30 mg/mmol) and depression (≥8) was 2.62 (95% 1.12–6.05) compared with a HR 1.34 (95% CI 1.04–1.74) with raised ACR only (Likelihood Ratio-test 0.03). Adding anxiety (≥8) to albuminuria (3–30) tripled the risk (HR 3.32 95% CI 1.43–7.17). The additive models suggest that these risks are not higher than expected based on each risk factor alone.

Conclusions
This study indicate that the risk of AMI in persons with elevated albuminuria but with an otherwise healthy CVD profile might be amplified by anxiety and depression symptoms. The increased risk with joint risk factors is not higher than expected based on each risk factor alone, which indicate that the risk factors do not share causal pathways.
Short-form development of the specific module of the QLICD-CRF(V2.0) for assessing the quality of life of patients with chronic renal failure
Authors: Xiao Zhengqin , Liu Yuxi , Fong Daniel Yee-Tak , Huang Xinping , Weng Min , Wan Chonghua 
Published: November 2022

Abstract
Background
A short instrument would enhance the viability of a study. Therefore, we aimed to shorten the specific module (SPD-10) of the Quality of Life Instrument for Chronic Diseases - Chronic Renal Failure (QLICD-CRF) for assessing the quality of life of patients with chronic renal failure.

Methods
The 10-item SPD-10 was self-administered to 164 patients with chronic renal failure. A shortened form was first obtained by a tandem use of the classical test theory (CTT), the generalizability theory (GT), and the item response theory (IRT). In addition, we also shortened the SPD-10 by the Optimal Test Assembly (OTA).

Results
Both the tandem use of GT, CTT and IRT, and the OTA derived the same 7-item shortened version (SPD-7). It included items CRF1, CRF2, CRF3, CRF4, CRF6, CRF8, and CRF9 of the SPD-10. The SPD-7 had a Cronbach alpha of 0.78. The correlation coefficients of its total and factor scores with those of the SPD-10 were 0.96 and 0.98, respectively. Confirmatory factor analysis confirmed the unidimensional structure of the SPD-7, with the comparative fit index=0.96, the Tucker-Lewis index=0.94, and the root mean square error of approximation=0.09.

Conclusion
The short-form SPD-7 is reliable and valid for assessing the impact of clinical symptoms and side effects on the quality of life of patients with chronic renal failure. It is an efficient option without compromising the measurement performance of the SPD-10.
Rapid and precise identification of bloodstream infections using a pre-treatment protocol combined with high-throughput multiplex genetic detection system
Authors: Zhang Jinghao , Yang Feng , Sun Zhaoyang , Fang Yi , Zhu Haowei , Zhang Dijun , Zeng Xianping , Liu Wenjian , Liu Tao , Liu Yixin , Chi Wenjing , Wang Su , Ding Li , Wu Yong , Zhang Yanmei , Zhao Hu 
Published: November 2022

Abstract
Background
Bloodstream infection (BSI) is a life-threatening condition with high morbidity and mortality rates worldwide. Early diagnosis of BSI is critical to avoid the unnecessary application of antimicrobial agents and for proper treatment. However, the current standard methods based on blood culture are time-consuming, thus failing to provide a timely etiological diagnosis of BSI, and common PCR-based detection might be inhibited by matrix components.

Methods
The current study explored an integrated pre-analytical treatment protocol for whole blood samples, wherein pathogens are enriched and purified by incubation and concentration, and inhibitors are inactivated and removed. Further, this study developed and evaluated a novel high-throughput multiplex genetic detection system (HMGS) to detect 24 of the most clinically prevalent BSI pathogens in blood culture samples and pre-treated whole blood samples. The specificity and sensitivity were evaluated using related reference strains and quantified bacterial/fungal suspensions. The clinical utility of BSI-HMGS combined with the pre-analytical treatment protocol was verified using blood cultures and whole blood samples.

Results
The combined pre-treatment protocol and BSI-HMGS was highly specific for target pathogens and possessed a low detection limit for clinical whole blood samples. The pre-treatment protocol could deplete the PCR inhibitors effectively. For blood culture samples, the current method showed 100.0% negative percent agreements and > 87.5% positive percent agreements compared to the reference results based on blood culture findings. For whole blood samples, the current method showed 100.0% negative percent agreements and > 80.0% positive percent agreements compared to the reference results for most pathogens. The turnaround time was ≤ 8 h, and all the procedures could be conducted in a general clinical laboratory.

Conclusion
The BSI-HMGS combined with the pre-treatment protocol was a practical and promising method for early and precise detection of BSIs, especially for areas without access to advanced medical facilities.
Low-dose nivolumab in advanced hepatocellular carcinoma
Authors: Chen Yen-Hao , Wang Chih-Chi , Chen Yen-Yang , Wang Jing-Houng , Hung Chao-Hung , Kuo Yuan-Hung 
Published: November 2022

Abstract
Background
The approved dose of nivolumab is 3 mg/kg or a flat dose of 240 mg for indications. There is no dose-response relationship for nivolumab; therefore, a low-dose regimen may be an option to reduce financial toxicity. This study was designed to investigate the efficacy and safety of low-dose nivolumab in the management of hepatocellular carcinoma (HCC).

Methods
We retrospectively reviewed patients with HCC who received 20 or 100 mg of nivolumab intravenously every 2 weeks. The objective response rate was determined in accordance with the Response Evaluation Criteria in Solid Tumors criteria version 1.1. The Cox regression model and Kaplan–Meier method were used to analyze hazard factors, progression-free survival (PFS), and overall survival (OS). Adverse events (AEs) were assessed according to the National Cancer Institute Common Terminology Criteria for Adverse Events version 5.0.

Results
In total, 78 patients were enrolled, including 49 with hepatitis B virus (HBV) and 23 with hepatitis C virus (HCV). All patients were staged as Barcelona Clinic Liver Cancer stage C, and 20 patients were classified as having Child–Pugh classification B (7). Nivolumab 20 mg was an independent prognostic factor for better PFS, and albumin-bilirubin grade 1 was the independent prognostic factor for superior OS in the multivariate analyses. Patients with better HBV (HBV DNA < 500 IU/ml) and HCV (HCV RNA undetectable) controls had superior OS. All AEs were grade 1–2 in severity, and all patients tolerated nivolumab without treatment interruption or dose adjustment. Additionally, 31 patients underwent subsequent therapy after nivolumab treatment.

Conclusion
Low-dose nivolumab may be effective with manageable toxicity and can be an alternative option to reduce financial toxicity in patients with advanced HCC who cannot afford the high cost of immune checkpoint inhibitors in real-world practice.