bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgically treated congenital cleft palate in a 4-month-old kitten: medium-term clinical and CT assessment
Authors: Garnier Paul , Viateau Véronique , Manassero Mathieu , Maurice Emeline 
Published: March 2022

Case summary A 4-month-old female domestic shorthair kitten was presented for a congenital cleft palate causing nasal discharge and sneezing episodes. CT revealed a palatal bone defect involving 20% of the palatal area. Surgical correction of both the hard and soft palate defects was performed using the overlapping and medially positioned flap techniques, respectively. Complete healing of the wound and full resolution of the clinical signs occurred within a 1-month period. At 2 months postoperatively, two punctiform oronasal fistulae were observed rostrally without associated clinical signs. Control CT, performed 6 months postoperatively, revealed a 50% enlargement of the palatal bone defect. At 12 months postoperatively, the cat was still in good general condition without any clinical signs. Relevance and novel information To the best of our knowledge, this is the first report to describe the treatment of a congenital cleft palate in a kitten using the overlapping flap technique with a successful medium-term clinical outcome, despite the formation of two oronasal fistulae. This suggests that, as in dogs, full restoration of oronasal compartmentation is not mandatory to achieve functional outcome. The increase of the palatal bone defect over time may play a role in late oronasal fistulae formation and should be considered for surgical planning.
Understanding information behavior of South Korean Twitter users who express suicidality on Twitter
Authors: Kim Donghun , Jung Woojin , Nam Seojin , Jeon Hongjin , Baek Jihyun , Zhu Yongjun 
Published: March 2022

Objective Although there were few studies on how suicidal users behave on Twitter, they only investigated partial aspects such as tweeting frequency and tweet length. Therefore, we aim to understand the various information behavior of suicidal users in South Korea. Methods To achieve this goal, we annotated 20,000 tweets and identified 1097 tweets with the expression of suicidality (i.e. suicidal tweets) and 229 suicidal users (i.e. experimental group). Using the data, a user profile analysis, comparative analysis with control group, and tweets/hashtags analysis were performed. Results Our results show that many suicidal users used suicide-related keywords in their user IDs, usernames, descriptions, and pinned tweets. We also found that, compared to the control group, the experimental group show different patterns of information behavior. The experimental group did not frequently use Twitter and, on average, wrote longer texts than the control group. A clear seasonal pattern was also identified in the experimental group's tweeting behavior. Frequently used keywords/hashtags were extracted from tweets written by the experimental group for the purpose of understanding their concerns and detecting more suicidal tweets. Conclusions We believe that our study will help in the understanding of suicidal users’ information behavior on social media and lay the basis for more accurate actions for suicide prevention and early intervention on social media.
The Patient Acceptable Symptom State as a Predictor of the Sports Activity Available State After Arthroscopic Rotator Cuff Repair
Authors: Kim Dong Min , Jeon In-Ho , Kim Ho Yeon , Park Jeong Hee , Kim Hyojune , Koh Kyoung Hwan 
Published: March 2022

Background: The patient acceptable symptom state (PASS) has emerged as a metric for evaluating patient satisfaction after treatment. There is little research on the relationship between sports activity and PASS values after arthroscopic rotator cuff repair (ARCR). Purpose: To (1) introduce the sports activity available state (SAAS) as an indicator of whether sports activities are possible based on patient symptoms after ARCR, (2) investigate the correlation between the SAAS and PASS, (3) predict the SAAS using derived PASS values, and (4) identify factors for achieving the PASS and SAAS. Study Design: Case-control study; Level of evidence, 3. Methods: Included were 201 patients who underwent ARCR between January 2015 and December 2016. At a mean follow-up of 38.7 ± 7.0 months, anchor questions were used to classify patients as SAAS+ (sports group) or SAAS– (nonsports group) and derive the PASS values for the pain visual analog scale (pVAS), American Shoulder and Elbow Surgeons (ASES), and Single Assessment Numeric Evaluation (SANE). The authors analyzed the correlation and difference between PASS and SAAS acquisition, and univariate and multivariate logistic regression analyses were performed to determine factors for PASS and SAAS achievement. Results: The final PASS values for the pVAS, ASES, and SANE were 0.5, 93.5, and 82.5, respectively. A significant correlation existed between PASS and SAAS acquisition (phi correlation coefficient, 0.647; P < .001). Sensitivity and specificity were >0.7 for all outcome scores when predicting SAAS using PASS values. A higher preoperative ASES score was significantly associated with achieving both the SAAS (OR, 1.032 [95% CI, 1.005-1.059]; P = .018) and PASS (OR, 2.556 [95% CI, 1.753-3.726]; P < .001). Diabetes (OR, 0.348 [95% CI, 0.130-0.931], P = .036) and a large to massive tear (OR, 0.378 [95% CI, 0.162-0.884]; P = .025) were significantly negatively associated with achieving the SAAS. Conclusion: The authors found the SAAS to be significantly correlated with the PASS. Also, SAAS was able to be predicted using the PASS value. Patients with higher preoperative ASES scores had higher odds of achieving both the PASS and SAAS, and patients with diabetes and those with large to massive tears had lower odds of achieving the SAAS.
Concurrent CDX2 cis-deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL
Authors: Passet Marie , Kim Rathana , Gachet Stéphanie , Sigaux François , Chaumeil Julie , Galland Ava , Sexton Thomas , Quentin Samuel , Hernandez Lucie , Larcher Lise , Bergugnat Hugo , Ye Tao , Karasu Nezih , Caye Aurélie , Heizmann Beate , Duluc Isabelle , Chevallier Patrice , Rousselot Philippe , Huguet Françoise , Leguay Thibaut , Hunault Mathilde , Pflumio Françoise , Freund Jean-Noël , Lobry Camille , Lhéritier Véronique , Dombret Hervé , Domon-Dell Claire , Soulier Jean , Boissel Nicolas , Clappier Emmanuelle 
Published: March 2022

Abstract
Oncogenic alterations underlying B-cell acute lymphoblastic leukemia (B-ALL) in adults remain incompletely elucidated. To uncover novel oncogenic drivers, we performed RNA sequencing and whole-genome analyses in a large cohort of unresolved B-ALL. We identified a novel subtype characterized by a distinct gene expression signature and the unique association of 2 genomic microdeletions. The 17q21.31 microdeletion resulted in a UBTF::ATXN7L3 fusion transcript encoding a chimeric protein. The 13q12.2 deletion resulted in monoallelic ectopic expression of the homeobox transcription factor CDX2, located 138 kb in cis from the deletion. Using 4C-sequencing and CRISPR interference experiments, we elucidated the mechanism of CDX2 cis-deregulation, involving PAN3 enhancer hijacking. CDX2/UBTF ALL (n = 26) harbored a distinct pattern of additional alterations including 1q gain and CXCR4 activating mutations. Within adult patients with Ph− B-ALL enrolled in GRAALL trials, patients with CDX2/UBTF ALL (n = 17/723, 2.4%) were young (median age, 31 years) and dramatically enriched in females (male/female ratio, 0.2, P = .002). They commonly presented with a pro-B phenotype ALL and moderate blast cell infiltration. They had poor response to treatment including a higher risk of failure to first induction course (19% vs 3%, P = .017) and higher post-induction minimal residual disease (MRD) levels (MRD ≥ 10−4, 93% vs 46%, P &lt; .001). This early resistance to treatment translated into a significantly higher cumulative incidence of relapse (75.0% vs 32.4%, P = .004) in univariate and multivariate analyses. In conclusion, we discovered a novel B-ALL entity defined by the unique combination of CDX2 cis-deregulation and UBTF::ATXN7L3 fusion, representing a high-risk disease in young adults.
Antibody-drug conjugates targeting CD248 inhibits liver fibrosis through specific killing on myofibroblasts
Authors: Liu Shaojie , Han Donghui , Xu Chao , Yang Fa , Li Yu , Zhang Keying , Zhao Xiaolong , Zhang Jiayu , Lu Tong , Lu Shiqi , Shi Changhong , Zhang Rui , Yang An-Gang , Zhao Aizhi , Qin Weijun , Yang Bo , Wen Weihong 
Published: March 2022

Abstract
Background
Chronic liver injury induces pathological repair, resulting in fibrosis, during which hepatic stellate cells (HSCs) are activated and transform into myofibroblasts. CD248 is mainly expressed on myofibroblasts and was considered as a promising target to treat fibrosis. The primary aim of this study was to generate a CD248 specific antibody-drug conjugate (ADC) and evaluate its therapeutic efficacy for liver fibrosis and its safety in vivo.

Methods
CD248 expression was examined in patients with liver cirrhosis and in mice with CCl4-induced liver fibrosis. The ADC IgG78-DM1, which targets CD248, was prepared and its bioactivity on activated primary HSCs was studied. The anti-fibrotic effects of IgG78-DM1 on liver fibrosis were evaluated in CCl4-induced mice. The reproductive safety and biosafety of IgG78-DM1 were also evaluated in vivo.

Results
CD248 expression was upregulated in patients with liver cirrhosis and in CCl4-induced mice, and was mainly expressed on alpha smooth muscle actin (α-SMA)+ myofibroblasts. IgG78-DM1 was successfully generated, which could effectively bind with and kill CD248+ activated HSCs in vitro and inhibit liver fibrosis in vivo. In addition, IgG78-DM1 was demonstrated to have qualified biosafety and reproductive safety in vivo.

Conclusions
Our study demonstrated that CD248 could be an ideal target for myofibroblasts in liver fibrosis, and CD248-targeting IgG78-DM1 had excellent anti-fibrotic effects in mice with liver fibrosis. Our study provided a novel strategy to treat liver fibrosis and expanded the application of ADCs beyond tumors.

Graphic Abstract
Pre-operative templating in THA using a short stem system: precision and accuracy of 2D versus 3D planning method
Authors: Reinbacher Patrick , Smolle Maria Anna , Friesenbichler Joerg , Draschl Alexander , Leithner Andreas , Maurer-Ertl Werner 
Published: March 2022

Abstract
Background
Total hip arthroplasty (THA) is the most successful orthopaedic surgery of the past century. The current study aimed to compare the accuracy of digital planning using 2D versus 3D templating.

Materials and methods
Ninety-five THAs in 90 patients were included in the current study. Pre- and post-operative X-rays (in two planes) and low-dose rotation computed tomography scans from hip to foot were performed. Paired t-test and regression analyses were conducted to compare 2D and 3D templating accuracy of the definitive implant.

Results
Cup size planned both with 2D (p < 0.0001) and 3D (p = 0.012) templating was significantly different from the definitively used cup size. The difference between the 2D-planned and implanted stem size (p < 0.0001) was statistically significant. In contrast, there were no significant differences in the 3D-planned and implanted stem size (p = 0.181). Three-dimensional templating showed significantly higher accuracy than 2D templating in terms of cup size (1.1 ± 1.4 versus 1.7 ± 1.8; p = 0.007) and stem size (0.3 ± 0.6 versus 0.7 ± 0.7; p < 0.0001).
With increasing body mass index (BMI), 2D templating of the stem became more inaccurate (p = 0.041). Remarkably, 3D templating remained accurate for all components (stem, p = 0.533; cup, p = 0.479) despite increasing BMI.

Conclusion
Despite extended planning time and increased exposure to radiation, 3D-based planning showed higher accuracy than 2D templating, especially in obese patients. On the basis of our results, we believe that 3D-based pre-operative planning in THA is justifiable and beneficial in patients with increased BMI.

Level of Evidence
III.
Data-independent acquisition mass spectrometry in severe rheumatic heart disease (RHD) identifies a proteomic signature showing ongoing inflammation and effectively classifying RHD cases
Authors: Salie M. Taariq , Yang Jing , Ramírez Medina Carlos R. , Zühlke Liesl J. , Chishala Chishala , Ntsekhe Mpiko , Gitura Bernard , Ogendo Stephen , Okello Emmy , Lwabi Peter , Musuku John , Mtaja Agnes , Hugo-Hamman Christopher , El-Sayed Ahmed , Damasceno Albertino , Mocumbi Ana , Bode-Thomas Fidelia , Yilgwan Christopher , Amusa Ganiyu A. , Nkereuwem Esin , Shaboodien Gasnat , Da Silva Rachael , Lee Dave Chi Hoo , Frain Simon , Geifman Nophar , Whetton Anthony D. , Keavney Bernard , Engel Mark E. ,   the RHDGen Network Consortium
Published: March 2022

AbstractBackgroundRheumatic heart disease (RHD) remains a major source of morbidity and mortality in developing countries. A deeper insight into the pathogenetic mechanisms underlying RHD could provide opportunities for drug repurposing, guide recommendations for secondary penicillin prophylaxis, and/or inform development of near-patient diagnostics.MethodsWe performed quantitative proteomics using Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectrometry (SWATH-MS) to screen protein expression in 215 African patients with severe RHD, and 230 controls. We applied a machine learning (ML) approach to feature selection among the 366 proteins quantifiable in at least 40% of samples, using the Boruta wrapper algorithm. The case–control differences and contribution to Area Under the Receiver Operating Curve (AUC) for each of the 56 proteins identified by the Boruta algorithm were calculated by Logistic Regression adjusted for age, sex and BMI. Biological pathways and functions enriched for proteins were identified using ClueGo pathway analyses.ResultsAdiponectin, complement component C7 and fibulin-1, a component of heart valve matrix, were significantly higher in cases when compared with controls. Ficolin-3, a protein with calcium-independent lectin activity that activates the complement pathway, was lower in cases than controls. The top six biomarkers from the Boruta analyses conferred an AUC of 0.90 indicating excellent discriminatory capacity between RHD cases and controls.ConclusionsThese results support the presence of an ongoing inflammatory response in RHD, at a time when severe valve disease has developed, and distant from previous episodes of acute rheumatic fever. This biomarker signature could have potential utility in recognizing different degrees of ongoing inflammation in RHD patients, which may, in turn, be related to prognostic severity.
A learning-based method to predict LncRNA-disease associations by combining CNN and ELM
Authors: Guo Zhen-Hao , Chen Zhan-Heng , You Zhu-Hong , Wang Yan-Bin , Yi Hai-Cheng , Wang Mei-Neng 
Published: March 2022

AbstractBackgroundlncRNAs play a critical role in numerous biological processes and life activities, especially diseases. Considering that traditional wet experiments for identifying uncovered lncRNA-disease associations is limited in terms of time consumption and labor cost. It is imperative to construct reliable and efficient computational models as addition for practice. Deep learning technologies have been proved to make impressive contributions in many areas, but the feasibility of it in bioinformatics has not been adequately verified.ResultsIn this paper, a machine learning-based model called LDACE was proposed to predict potential lncRNA-disease associations by combining Extreme Learning Machine (ELM) and Convolutional Neural Network (CNN). Specifically, the representation vectors are constructed by integrating multiple types of biology information including functional similarity and semantic similarity. Then, CNN is applied to mine both local and global features. Finally, ELM is chosen to carry out the prediction task to detect the potential lncRNA-disease associations. The proposed method achieved remarkable Area Under Receiver Operating Characteristic Curve of 0.9086 in Leave-one-out cross-validation and 0.8994 in fivefold cross-validation, respectively. In addition, 2 kinds of case studies based on lung cancer and endometrial cancer indicate the robustness and efficiency of LDACE even in a real environment.ConclusionsSubstantial results demonstrated that the proposed model is expected to be an auxiliary tool to guide and assist biomedical research, and the close integration of deep learning and biology big data will provide life sciences with novel insights.
Starvation causes changes in the intestinal transcriptome and microbiome that are reversed upon refeeding
Authors: Jawahar Jayanth , McCumber Alexander W. , Lickwar Colin R. , Amoroso Caroline R. , de la Torre Canny Sol Gomez , Wong Sandi , Morash Margaret , Thierer James H. , Farber Steven A. , Bohannan Brendan J. M. , Guillemin Karen , Rawls John F. 
Published: March 2022

Abstract
Background
The ability of animals and their microbiomes to adapt to starvation and then restore homeostasis after refeeding is fundamental to their continued survival and symbiosis. The intestine is the primary site of nutrient absorption and microbiome interaction, however our understanding of intestinal adaptations to starvation and refeeding remains limited. Here we used RNA sequencing and 16S rRNA gene sequencing to uncover changes in the intestinal transcriptome and microbiome of zebrafish subjected to long-term starvation and refeeding compared to continuously fed controls.

Results
Starvation over 21 days led to increased diversity and altered composition in the intestinal microbiome compared to fed controls, including relative increases in Vibrio and reductions in Plesiomonas bacteria. Starvation also led to significant alterations in host gene expression in the intestine, with distinct pathways affected at early and late stages of starvation. This included increases in the expression of ribosome biogenesis genes early in starvation, followed by decreased expression of genes involved in antiviral immunity and lipid transport at later stages. These effects of starvation on the host transcriptome and microbiome were almost completely restored within 3 days after refeeding. Comparison with published datasets identified host genes responsive to starvation as well as high-fat feeding or microbiome colonization, and predicted host transcription factors that may be involved in starvation response.

Conclusions
Long-term starvation induces progressive changes in microbiome composition and host gene expression in the zebrafish intestine, and these changes are rapidly reversed after refeeding. Our identification of bacterial taxa, host genes and host pathways involved in this response provides a framework for future investigation of the physiological and ecological mechanisms underlying intestinal adaptations to food restriction.
Comparative study of vestibular projection pathway connectivity in cerebellar injury patients and healthy adults
Authors: Gam Byeong Uk , Cho In Hee , Yeo Sang Seok , Kwon Jung Won , Jang Sung Ho , Oh Seunghue 
Published: March 2022

Abstract
Objective
Cerebellar injury can not only cause gait and postural instability, nystagmus, and vertigo but also affect the vestibular system. However, changes in connectivity regarding the vestibular projection pathway after cerebellar injury have not yet been reported. Therefore, in the current study, we investigated differences in the connectivity of the vestibular projection pathway after cerebellar injury using diffusion tensor imaging (DTI) tractography.

Methods
We recruited four stroke patients with cerebellar injury. Neural connectivity in the vestibular nucleus (VN) of the pons and medulla oblongata in patients with cerebellar injury was measured using DTI. Connectivity was defined as the incidence of connection between the VN on the pons and medulla oblongata and target brain regions such as the cerebellum, thalamus, parieto-insular vestibular cortex (PIVC), and parietal lobe.

Results
At thresholds of 10 and 30, there was lower connectivity in the ipsilateral hemisphere between the VN at the medullar level and thalamus in the patients than in healthy adults. At a threshold of 1 and 10, the patient group showed lower VN connectivity with the PIVC than healthy adults. At a threshold of 1, VN connectivity with the parietal lobe in the contralateral hemisphere was lower in the patients than in healthy adults. Additionally, at a threshold of 30, VN connectivity at the pons level with the cerebellum was lower in healthy adults than in the patients.

Conclusion
Cerebellar injury seems to be associated with decreased vestibular projection pathway connectivity, especially in the ipsilateral thalamus, PIVC, and contralateral parietal lobe.
Wound-induced signals regulate root organogenesis in Arabidopsis explants
Authors: Shin Seung Yong , Park Su-Jin , Kim Hyun-Soon , Jeon Jae-Heung , Lee Hyo-Jun 
Published: March 2022

Abstract
Background
Reactive oxygen species (ROS) and calcium ions (Ca2+) are representative signals of plant wound responses. Wounding triggers cell fate transition in detached plant tissues and induces de novo root organogenesis. While the hormonal regulation of root organogenesis has been widely studied, the role of early wound signals including ROS and Ca2+ remains largely unknown.

Results
We identified that ROS and Ca2+ are required for de novo root organogenesis, but have different functions in Arabidopsis explants. The inhibition of the ROS and Ca2+ signals delayed root development in detached leaves. Examination of the auxin signaling pathways indicated that ROS and Ca2+ did not affect auxin biosynthesis and transport in explants. Additionally, the expression of key genes related to auxin signals during root organogenesis was not significantly affected by the inhibition of ROS and Ca2+ signals. The addition of auxin partially restored the suppression of root development by the ROS inhibitor; however, auxin supplementation did not affect root organogenesis in Ca2+-depleted explants.

Conclusions
Our results indicate that, while both ROS and Ca2+ are key molecules, at least in part of the auxin signals acts downstream of ROS signaling, and Ca2+ acts downstream of auxin during de novo root organogenesis in leaf explants.