bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ureteroscopic treatment of urolithiasis: How do we measure and optimise outcomes?
Authors: Smith Daron , Rossi Sabrina Helena , Smith Yuko , Pietropaolo Amelia , Joshi Hrishi , Ratan Hari 
Published: April 2024

Background: Patients with urolithiasis have access to a wide range of efficacious therapeutic surgical options, including shockwave lithotripsy (SWL), retrograde ureteric or intrarenal surgery with semi-rigid and flexible ureteroscopes (URS or fURS) and percutaneous nephrolithotomy (PCNL). In recent years, there have been many peer-reviewed publications evaluating new techniques and new equipment, such as pulse-modulated Holmium:YAG and thulium fibre lasers. However, when reviewing this extensive literature, it becomes apparent that there is no consensus on what constitutes a ‘successful’ stone treatment outcome. Objectives: The purpose of this article is to review the existing measures of ‘success’ after the ureteroscopic treatment of urolithiasis and to promote a standardised and holistic approach to reporting outcomes in clinical trials. Methods: Our narrative review focussed on studies examining measures of success in urolithiasis treatment published within the last 10 years. Conclusions: Due to markedly different reported outcome measures of treatments for urolithiasis, comparing results between studies can be difficult. In addition to measuring clinical outcomes, there is an increasing acknowledgement of the importance of patient-reported outcome measures (PROMs) in determining treatment success, and the need to consider the cost-effectiveness and environmental sustainability of various treatments. We suggest that all future studies on this common urological condition should incorporate holistic and tranpsarent outcome measures. Level of evidence: Not applicable
Comparison of Pain Scores and Functional Outcomes of Patients Undergoing Arthroscopic Hip Labral Repair and Concomitant Capsular Repair or Plication Versus No Closure
Authors: Bindi Victoria E. , Hao Kevin A. , Freeman David A. , Olowofela Bankole O. , Moser Michael W. , Farmer Kevin W. , Pazik Marissa , Roach Ryan P. 
Published: April 2024

Background: The need for capsular closure during arthroscopic hip labral repair is debated. Purpose: To compare pain and functional outcomes in patients undergoing arthroscopic hip labral repair with concomitant repair or plication of the capsule versus no closure. Study Design: Cohort study. Methods: Outcomes were compared between patients undergoing arthroscopic hip labral repair with concomitant repair or plication of the capsule versus no closure at up to 2 years postoperatively and with stratification by age and sex. Patients with lateral center-edge angle <20°, a history of instability, a history of prior arthroscopic surgery in the ipsilateral hip, or a history of labral debridement only were excluded. Subanalysis was performed between patients undergoing no capsular closure who were propensity score matched 1:1 with patients undergoing repair or plication based on age, sex, and preoperative Modified Harris Hip Score (MHHS). We compared patients who underwent T-capsulotomy with concomitant capsular closure matched 1:5 with patients who underwent an interportal capsulotomy with concomitant capsular repair based on age, sex, and preoperative MHHS. Results: Patients undergoing capsular closure (n = 1069), compared with the no-closure group (n = 230), were more often female (68.6% vs 53.0%, respectively; P < .001), were younger (36.4 ± 13.3 vs 47.9 ± 14.7 years; P < .001), and had superior MHHS scores at 2 years postoperatively (85.8 ± 14.5 vs 81.8 ± 18.4, respectively; P = .020). In the matched analysis, no difference was found in outcome measures between patients in the capsular closure group (n = 215) and the no-closure group (n = 215) at any follow-up timepoint. No significant difference was seen between the 2 closure techniques at any follow-up timepoint. Patients with closure of the capsule achieved the minimal clinically important difference (MCID) and the patient acceptable symptom state (PASS) for the 1-year MHHS at a similar rate as those without closure (MCID, 50.3% vs 44.9%, P = .288; PASS, 56.8% vs 51.1%, P = .287, respectively). Patients with T-capsulotomy achieved the MCID and the PASS for the 1-year MHHS at a similar rate compared with those with interportal capsulotomy (MCID, 50.1% vs 44.9%, P = .531; PASS, 65.7% vs 61.2%, P = .518, respectively). Conclusion: When sex, age, and preoperative MHHS were controlled, capsular closure and no capsular closure after arthroscopic hip labral repair were associated with similar pain and functional outcomes for patients up to 2 years postoperatively.
Standardized indolent systemic mastocytosis evaluations across a health care system: implications for screening accuracy
Authors: McMurray Jeremy C. , Pacheco Curtis S. , Schornack Brandon J. , Sun Xiaoping , Brunader Janet A. , Scott Alexis E. , Ariza Juan S. , Kou Chung-Ting J. , Costantino Ryan C. , Pittman Luke M. , Adams Karla E. , Waters Aubri M. , Pryor Eric M. , Lyons Jonathan J. , Metcalfe Dean D. , Maric Irina , Boggs Nathan A. 
Published: April 2024

Abstract
Timely diagnosis of systemic mastocytosis (SM) remains challenging because of care heterogeneity. We implemented a standardized approach for SM screening and diagnosis using a novel health care system–wide international screening registry. A retrospective analysis assessed rates of SM, cutaneous mastocytosis (CM), and molecular diagnoses before and 2 years after care standardization. The accuracy of individual and combined SM screening tests, basal serum tryptase (BST) ≥11.5 and ≥20.0 ng/mL, REMA ≥2, monomorphic maculopapular CM (MPCM), and elevated BST based upon tryptase genotype, was analyzed. Tryptase genotyping and high-sensitivity KIT p.D816V testing increased substantially 2 years after care standardization. SM diagnoses doubled from 47 to 94, and KIT p.D816V molecular diagnoses increased from 24 to 79. Mean BST and KIT p.D816V variant allele frequency values were significantly lower in patients diagnosed after standardization. Hereditary-alpha tryptasemia prevalence was increased in SM before care standardization (4/30 [13.3%]) but reflected the general population prevalence 2 years later at (5/76 [6.6%]). Elevated BST based upon genotype and BST ≥11.5 ng/mL had the highest sensitivities at 84.2% and 88.3%, respectively. The presence of monomorphic MPCM, elevated BST based upon tryptase genotype, and the combination of REMA ≥2 with elevated BST based upon tryptase genotype had specificities &gt;90%. BST &gt;20.0 ng/mL had low sensitivity and specificity and was not required to establish any indolent SM (ISM) diagnosis. Care standardization increased SM diagnosis rates, particularly in patients with low BSTs. Stratifying BST based upon genotype had the best overall sensitivity and specificity of any ISM screening test and improved the REMA score specificity.
Real-world and clinical trial outcomes in large B-cell lymphoma with axicabtagene ciloleucel across race and ethnicity
Authors: Locke Frederick L. , Siddiqi Tanya , Jacobson Caron A. , Ghobadi Armin , Ahmed Sairah , Miklos David B. , Perales Miguel-Angel , Munoz Javier , Fingrut Warren B. , Pennisi Martina , Gauthier Jordan , Shadman Mazyar , Gowda Lohith , Mirza Abu-Sayeef , Abid Muhammad Bilal , Hong Sanghee , Majhail Navneet S. , Kharfan-Dabaja Mohamed A. , Khurana Arushi , Badar Talha , Lin Yi , Bennani N. Nora , Herr Megan M. , Hu Zhen-Huan , Wang Hai-Lin , Baer Anjani , Baro Elande , Miao Harry , Spooner Clare , Xu Hairong , Pasquini Marcelo C. 
Published: April 2024

Abstract
Axicabtagene ciloleucel (axi-cel) is an autologous anti-CD19 chimeric antigen receptor (CAR) T-cell therapy approved for relapsed/refractory (R/R) large B-cell lymphoma (LBCL). Despite extensive data supporting its use, outcomes stratified by race and ethnicity groups are limited. Here, we report clinical outcomes with axi-cel in patients with R/R LBCL by race and ethnicity in both real-world and clinical trial settings. In the real-world setting, 1290 patients who received axi-cel between 2017 and 2020 were identified from the Center for International Blood and Marrow Transplant Research database; 106 and 169 patients were included from the ZUMA-1 and ZUMA-7 trials, respectively. Overall survival was consistent across race/ethnicity groups. However, non-Hispanic (NH) Black patients had lower overall response rate (OR, 0.37; 95% CI, 0.22-0.63) and lower complete response rate (OR, 0.57; 95% CI, 0.33-0.97) than NH White patients. NH Black patients also had a shorter progression-free survival vs NH White (HR, 1.41; 95% CI, 1.04-1.90) and NH Asian patients (HR, 1.67; 95% CI, 1.08-2.59). NH Asian patients had a longer duration of response than NH White (HR, 0.56; 95% CI, 0.33-0.94) and Hispanic patients (HR, 0.54; 95% CI, 0.30-0.97). There was no difference in cytokine release syndrome by race/ethnicity; however, higher rates of any-grade immune effector cell–associated neurotoxicity syndrome were observed in NH White patients than in other patients. These results provide important context when treating patients with R/R LBCL with CAR T-cell therapy across different racial and ethnic groups. ZUMA-1 and ZUMA-7 (ClinicalTrials.gov identifiers: #NCT02348216 and #NCT03391466, respectively) are registered on ClinicalTrials.gov.
An economic evaluation of eptinezumab for the preventive treatment of migraine in the UK, with consideration for natural history and work productivity
Authors: Griffin Edward , Shirley Gawain , Lee Xin Ying , Awad Susanne F. , Tyagi Alok , Goadsby Peter J. 
Published: April 2024

Abstract
Background
Migraine is a highly prevalent neurological disease with a substantial societal burden due to lost productivity. From a societal perspective, we assessed the cost-effectiveness of eptinezumab for the preventive treatment of migraine.

Methods
An individual patient simulation of discrete competing events was developed to evaluate eptinezumab cost-effectiveness compared to best supportive care for adults in the United Kingdom with ≥ 4 migraine days per month and prior failure of ≥ 3 preventive migraine treatments. Individuals with sampled baseline characteristics were created to represent this population, which comprised dedicated episodic and chronic migraine subpopulations. Clinical efficacy, utility, and work productivity inputs were based on results from the DELIVER randomised controlled trial (NCT04418765). Timing of natural history events and treatment holidays—informed by the literature—were simulated to unmask any natural improvement of the disease unrelated to treatment. The primary outcomes were monthly migraine days, migraine-associated costs, quality-adjusted life years (QALYs), incremental cost-effectiveness ratio, and net monetary benefit, each evaluated over a 5-year time horizon from 2020. Secondary analyses explored a lifetime horizon and an alternative treatment stopping rule.

Results
Treatment with eptinezumab resulted in an average of 0.231 QALYs gained at a saving of £4,894 over 5 years, making eptinezumab dominant over best supportive care (i.e., better health outcomes and less costly). This result was confirmed by the probabilistic analysis and all alternative assumption scenarios under the same societal perspective. Univariate testing of inputs showed net monetary benefit was most sensitive to the number of days of productivity loss, and monthly salary.

Conclusions
This economic evaluation shows that from a societal perspective, eptinezumab is a cost-effective treatment in patients with ≥ 4 migraine days per month and for whom ≥ 3 other preventive migraine treatments have failed.

Trial registration
N/A.

Graphical Abstract
Functional and oncological outcomes of patients with proximal humerus osteosarcoma managed by limb salvage
Authors: Sadek Wael Mohamed Safwat , Elshamly Ibrahim Khairy Fayed , Salem Moustafa Saladin Mohammed , AbouSenna Wessam Gamal , Ebeid Emad , Ebeid Walid Atef 
Published: April 2024

Abstract
Background
Osteosarcoma is the most common primary bone malignancy in skeletally immature patients. The proximal humerus is the third most common site of osteosarcoma. The literature shows a paucity of published data concerning the outcome of proximal humerus osteosarcoma managed by limb salvage. The purpose of this study was to answer the following questions: (1) do patients with proximal humerus osteosarcoma managed by limb salvage and neoadjuvant chemotherapy show good functional and oncological outcomes, and (2) are there any prognostic factors that are associated with better oncological and functional outcomes?

Materials and methods
The study was a retrospective case series study assessing the overall outcome of 34 patients with proximal humerus osteosarcoma. Eighteen patients were males (53%) while 16 were females. Biological reconstruction was done in 15 patients (44%), while nonbiological reconstruction was done in 19 patients. Resections were mainly intraarticular (82%). Functional outcome was assessed using the Musculoskeletal Tumor Society (MSTS) score, while oncological outcome was assessed based on local recurrence and development of chest metastasis. Comparisons between quantitative variables were done using the nonparametric Mann–Whitney test. To compare categorical data, the chi-square (χ2) test was performed. The exact test was used instead when the expected frequency was less than 5. Correlations between quantitative variables were examined using the Spearman correlation coefficient.

Results
The mean MSTS score was 25.5 (range 23–29). A younger age was statistically correlated with a poorer MSTS score (P = 0.0016). Six patients out of 34 (17.6%) had local recurrence and four of them (67%) were treated by forequarter amputation. 41% of patients developed chest metastasis, and the majority of them were treated by chemotherapy (71%). In comparison with patients with osteosarcoma at other sites who were also managed in our institution, proximal humerus osteosarcoma patients showed higher incidence rates of local recurrence and chest metastasis along with lower 5-year patient and limb survivorships compared to distal femur, proximal tibia and proximal femur osteosarcoma patients.

Conclusion
Treatment of osteosarcoma of the proximal humerus by limb salvage and chemotherapy yields a good functional outcome. The method of reconstruction does not impact the resultant function. The 5-year survivorship of these patients is 65%. Younger patients have a better oncological outcome and an inferior functional outcome.

Level of evidence
Level IV therapeutic study.
TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing
Authors: Hu Jianqiao , Luo Sai , Tian Ming , Ye Adam Yongxin 
Published: April 2024

Abstract
Background
High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, ‘N’s. PCR duplicates introduced in library preparation are conventionally removed in genomics studies, and several deduplication tools have been developed for this purpose. Two identical reads may appear different due to ambiguous bases and the existing tools cannot address ‘N’s correctly or efficiently.

Results
Here we proposed and implemented TrieDedup, which uses the trie (prefix tree) data structure to compare and store sequences. TrieDedup can handle ambiguous base ‘N’s, and efficiently deduplicate at the level of raw sequences. We also reduced its memory usage by approximately 20% by implementing restrictedDict in Python. We benchmarked the performance of the algorithm and showed that TrieDedup can deduplicate reads up to 270-fold faster than pairwise comparison at a cost of 32-fold higher memory usage.

Conclusions
The TrieDedup algorithm may facilitate PCR deduplication, barcode or UMI assignment, and repertoire diversity analysis of large-scale high-throughput sequencing datasets with its ultra-fast algorithm that can account for ambiguous bases due to sequencing errors.
Girdling behavior of the longhorn beetle modulates the host plant to enhance larval performance
Authors: Choi Min-Soo , Lee Juhee , Kim Jeong-Min , Kim Sang-Gyu , Joo Youngsung 
Published: April 2024

Abstract
Background
Preingestive behavioral modulations of herbivorous insects on the host plant are abundant over insect taxa. Those behaviors are suspected to have functions such as deactivation of host plant defenses, nutrient accumulation, or modulating plant-mediated herbivore interactions. To understand the functional consequence of behavioral modulation of insect herbivore, we studied the girdling behavior of Phytoecia rufiventris Gautier (Lamiinae; Cerambycidae) on its host plant Erigeron annuus L. (Asteraceae) that is performed before endophytic oviposition in the stem.

Results
The girdling behavior significantly increased the larval performance in both field monitoring and lab experiment. The upper part of the girdled stem exhibited lack of jasmonic acid induction upon larval attack, lowered protease inhibitor activity, and accumulated sugars and amino acids in compared to non-girdled stem. The girdling behavior had no effect on the larval performance of a non-girdling longhorn beetle Agapanthia amurensis, which also feeds on the stem of E. annuus during larval phase. However, the girdling behavior decreased the preference of A. amurensis females for oviposition, which enabled P. rufiventris larvae to avoid competition with A. amurensis larvae.

Conclusions
In conclusion, the girdling behavior modulates plant physiology and morphology to provide a modulated food source for larva and hide it from the competitor. Our study implies that the insect behavior modulations can have multiple functions, providing insights into adaptation of insect behavior in context of plant-herbivore interaction.
Screening of temperature-responsive signalling molecules during sex differentiation in Asian yellow pond turtle (Mauremys mutica)
Authors: Liu Xiaoli , Xu Haoyang , Peng Mingwei , Zhou Chenyao , Wei Chengqing , Hong Xiaoyou , Li Wei , Chen Chen , Ji Liqin , Zhu Xinping 
Published: April 2024

Abstract
Background
The Asian yellow pond turtle (Mauremys mutica) is an important commercial freshwater aquaculture species in China. This species is a highly sexually dimorphic species, with males growing at a faster rate than females and exhibits temperature-dependent sex determination (TSD), in which the incubation temperature during embryonic development determines the sexual fate. However, the mechanisms of the sex determination or sex differentiation in the Asian yellow pond turtle are remain a mystery.

Results
Temperature-specific gonadal transcriptomics of the Asian yellow pond turtle were performed during the thermosensitive period (stage 15) using RNA-seq technology to identify candidate genes that initiate gonadal differentiation. We uncovered candidates that were the first to respond to temperature. These candidates were sexually dimorphic in expression, reflecting differences in gonadal (Cirbp, Runx1) and germline differentiation (Vasa, Nanos1, Piwil2), gametogenesis (Hmgb3, Zar1, Ovoinhibitor-like, Kif4), steroid hormone biosynthesis (Hsd17b5, Hsd17b6), heat shock (Dnajb6, Hsp90b1, Hsp90aa1) and transient receptor potential channel genes (Trpm1, Trpm4, Trpm6, Trpv1).

Conclusions
Our work will provide important genetic information to elucidate the mechanisms of sex control in the Asian yellow pond turtles, and will contribute important genetic resources for further studies of temperature-dependent sex determination in turtles.
Genome-wide identification and expression pattern analysis of the Aux/IAA (auxin/indole-3-acetic acid) gene family in alfalfa (Medicago sativa) and the potential functions under drought stress
Authors: Zhang Jinqing , Li Shuxia , Gao Xueqin , Liu Yaling , Fu BingZhe 
Published: April 2024

Abstract
Background
Auxin/induced-3-acetic acid (Aux/IAA) is an important plant hormone that affects plant growth and resistance to abiotic stresses. Drought stress is a vital factor in reducing plant biomass yield and production quality. Alfalfa (Medicago sativa L.) is the most widely planted leguminous forage and one of the most economically valuable crops in the world. Aux/IAA is one of the early responsive gene families of auxin, playing a crucial role in response to drought stress. However, the characteristics of the Aux/IAA gene family in alfalfa and its potential function in response to drought stress are still unknown.

Result
A total of 41 Aux/IAA gene members were identified in alfalfa genome. The physicochemical, peptide structure, secondary and tertiary structure analysis of proteins encoded by these genes revealed functional diversity of the MsIAA gene. A phylogenetic analysis classified the MsIAA genes into I-X classes in two subgroups. And according to the gene domain structure, these genes were classified into typical MsIAA and atypical MsIAA. Gene structure analysis showed that the MsIAA genes contained 1–4 related motifs, and except for the third chromosome without MsIAAs, they were all located on 7 chromosomes. The gene duplication analysis revealed that segmental duplication and tandem duplication greatly affected the amplification of the MsIAA genes. Analysis of the Ka/Ks ratio of duplicated MsAux/IAA genes suggested purification selection pressure was high and functional differences were limited. In addition, identification and classification of promoter cis-elements elucidated that MsIAA genes contained numerous elements associated to phytohormone response and abiotic stress response. The prediction protein–protein interaction network showed that there was a complex interaction between the MsAux/IAA genes. Gene expression profiles were tissue-specific, and MsAux/IAA had a broad response to both common abiotic stress (ABA, salt, drought and cold) and heavy metal stress (Al and Pb). Furthermore, the expression patterns analysis of 41 Aux/IAA genes by the quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that Aux/IAA genes can act as positive or negative factors to regulate the drought resistance in alfalfa.

Conclusion
This study provides useful information for the alfalfa auxin signaling gene families and candidate evidence for further investigation on the role of Aux/IAA under drought stress. Future studies could further elucidate the functional mechanism of the MsIAA genes response to drought stress.