bluuebunny/crossref_metadata_2025_split huggingface dataset:
Como ver o que nos olha?
Authors: Mirocznik Betty 
Published: December 2023

Esse artigo tem como foco central a análise das rasgaduras e aparições, e do paradoxo entre o modo de presença das coisas em relação à percepção que delas podemos ter. Isto é, o modo da presença ausente que revela ser o processo perceptivo marcado pela ambiguidade. Para tanto, me debruço sobre a apropriação dos espaços arquitetônicos pelo sujeito na construção de um lugar singular, tomando como estudo de caso o projeto do escritório japonês SANAA para o Campus Vitra (2006) em Weil am Rhein na Alemanha, por sua configuração única. Com vistas a dar conta dessa narrativa, visitei o Campus Vitra, com o intuito de experimentar, vivenciar e comprovar se a prática projetual e construtiva de Kazuyo Sejima e Ryue Nishizawa, opera de fato em sentido contrário ao mainstream, e, como sua arquitetura pode ou não transformar a relação e a percepção do fruidor com o entorno. Como fortuna crítica remeto às reflexões do arquiteto finlandês Juhani Pallasmaa (1936), relacionada a apreensão psíquica da arquitetura obtida a partir do conceito de atmosfera – como um espaço sintonizado composto por um conjunto de elementos indefinidos e espacialmente distribuídos – e ao conceito da fenomenologia focada na atmosfera sob o ponto de vista do filósofo alemão Gernot Böhme. Para o filósofo, a atmosfera não se refere a características espirituais, mas a uma atitude reflexiva e crítica relacionada à consciência da corporeidade e da percepção do indivíduo.
ApoA-I Protects Pancreatic β-Cells From Cholesterol-Induced Mitochondrial Damage and Restores Their Ability to Secrete Insulin
Authors: Manandhar Bikash , Pandzic Elvis , Deshpande Nandan , Chen Sing-Young , Wasinger Valerie C. , Kockx Maaike , Glaros Elias N. , Ong Kwok Leung , Thomas Shane R. , Wilkins Marc R. , Whan Renee M. , Cochran Blake J. , Rye Kerry-Anne 
Published: December 2023

BACKGROUND:
High cholesterol levels in pancreatic β-cells cause oxidative stress and decrease insulin secretion. β-cells can internalize apo (apolipoprotein) A-I, which increases insulin secretion. This study asks whether internalization of apoA-I improves β-cell insulin secretion by reducing oxidative stress.

METHODS:
Ins-1E cells were cholesterol-loaded by incubation with cholesterol-methyl-β-cyclodextrin. Insulin secretion in the presence of 2.8 or 25 mmol/L glucose was quantified by radioimmunoassay. Internalization of fluorescently labeled apoA-I by β-cells was monitored by flow cytometry. The effects of apoA-I internalization on β-cell gene expression were evaluated by RNA sequencing. ApoA-I-binding partners on the β-cell surface were identified by mass spectrometry. Mitochondrial oxidative stress was quantified in β-cells and isolated islets with MitoSOX and confocal microscopy.

RESULTS:

An F
1
-ATPase β-subunit on the β-cell surface was identified as the main apoA-I-binding partner. β-cell internalization of apoA-I was time-, concentration-, temperature-, cholesterol-, and F
1
-ATPase β-subunit-dependent. β-cells with internalized apoA-I (apoA-I
+
cells) had higher cholesterol and cell surface F
1
-ATPase β-subunit levels than β-cells without internalized apoA-I (apoA-I
−
cells). The internalized apoA-I colocalized with mitochondria and was associated with reduced oxidative stress and increased insulin secretion. The IF
1
(ATPase inhibitory factor 1) attenuated apoA-I internalization and increased oxidative stress in Ins-1E β-cells and isolated mouse islets. Differentially expressed genes in apoA-I
+
and apoA-I
−
Ins-1E cells were related to protein synthesis, the unfolded protein response, insulin secretion, and mitochondrial function.

CONCLUSIONS:
These results establish that β-cells are functionally heterogeneous, and apoA-I restores insulin secretion in β-cells with elevated cholesterol levels by improving mitochondrial redox balance.
Spatial-extent inference for testing variance components in reliability and heritability studies
Authors: Pan Ruyi , Dickie Erin W. , Hawco Colin , Reid Nancy , Voineskos Aristotle N. , Park Jun Young 
Published: December 2023

Abstract
Clusterwise inference is a popular approach in neuroimaging to increase sensitivity, but most existing methods are currently restricted to the General Linear Model (GLM) for testing mean parameters. Statistical methods for testing variance components, which are critical in neuroimaging studies that involve estimation of narrow-sense heritability or test-retest reliability, are underdeveloped due to methodological and computational challenges, which would potentially lead to low power. We propose a fast and powerful test for variance components called CLEAN-V (CLEAN for testing Variance components). CLEAN-V models the global spatial dependence structure of imaging data and computes a locally powerful variance component test statistic by data-adaptively pooling neighborhood information. Correction for multiple comparisons is achieved by permutations to control family-wise error rate (FWER). Through analysis of task-functional magnetic resonance imaging (fMRI) data from the Human Connectome Project across five tasks and comprehensive data-driven simulations, we show that CLEAN-V outperforms existing methods in detecting test-retest reliability and narrow-sense heritability with significantly improved power, with the detected areas aligning with activation maps. The computational efficiency of CLEAN-V also speaks of its practical utility, and it is available as an R package.
Denoising diffusion MRI: Considerations and implications for analysis
Authors: Manzano Patron Jose Pedro , Moeller Steen , Andersson Jesper L.R. , Ugurbil Kamil , Yacoub Essa , Sotiropoulos Stamatios N. 
Published: December 2023

Abstract
Development of diffusion MRI (dMRI) denoising approaches has experienced considerable growth over the last years. As noise can inherently reduce accuracy and precision in measurements, its effects have been well characterised both in terms of uncertainty increase in dMRI-derived features and in terms of biases caused by the noise floor, the smallest measurable signal given the noise level. However, gaps in our knowledge still exist in objectively characterising dMRI denoising approaches in terms of both of these effects and assessing their efficacy. In this work, we reconsider what a denoising method should and should not do and we accordingly define criteria to characterise the performance. We propose a comprehensive set of evaluations, including i) benefits in improving signal quality and reducing noise variance, ii) gains in reducing biases and the noise floor and improving, iii) preservation of spatial resolution, iv) agreement of denoised data against a gold standard, v) gains in downstream parameter estimation (precision and accuracy), and vi) efficacy in enabling noise-prone applications, such as ultra-high-resolution imaging. We further provide newly acquired complex datasets (magnitude and phase) with multiple repeats that sample different SNR regimes to highlight performance differences under different scenarios. Without loss of generality, we subsequently apply a number of exemplar patch-based denoising algorithms to these datasets, including Non-Local Means, Marchenko-Pastur PCA (MPPCA) in the magnitude and complex domain, and NORDIC, and compare them with respect to the above criteria and against a gold standard complex average of multiple repeats. We demonstrate that all tested denoising approaches reduce noise-related variance, but not always biases from the elevated noise floor. They all induce a spatial resolution penalty, but its extent can vary depending on the method and the implementation. Some denoising approaches agree with the gold standard more than others and we demonstrate challenges in even defining such a standard. Overall, we show that dMRI denoising performed in the complex domain is advantageous to magnitude domain denoising with respect to all the above criteria.
Assessment of lower extremity venous insufficiency and lipedema and their association with knee symptoms, functions, and quality of life in patients with knee osteoarthritis
Authors: Ekti Hilmi , Toktas Hasan , Yesil Hilal , Kaya Furkan 
Published: December 2023

Objective To evaluate the effects of the venous insufficiency (VI) or lipedema on the symptoms, functions, and quality of life (QoL) of patients with knee osteoarthritis (OA). Methods 96 patients with stage 3/4 knee OA were included in the study. Patients were grouped as OA ( n = 35), VI + OA ( n = 35), and lipedema + OA ( n = 26). Range of motion (ROM), Visual Analogue Scale (VAS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), short-form (SF-36), and 6-minute walking test (6MWT) were evaluated. Results WOMAC stiffness score was significantly higher in the VI group than the other groups ( p < .05). VAS resting, WOMAC pain, function, and total scores were significantly higher in the lipedema + OA and VI + OA groups than the OA group ( p < .05). SF-36-physical role limitation was significantly lower in the lipedema and VI groups ( p < .05). Conclusion VI or lipedema accompanying knee OA increases the existing disability due to OA by negatively affecting patients regarding pain, QoL, and physical functioning.
Renoprotective effects of combination treatment with sodium-glucose cotransporter inhibitors and GLP-1 receptor agonists in patients with type 2 diabetes mellitus according to preceding medication
Authors: Kobayashi Kazuo , Toyoda Masao , Tone Atsuhito , Kawanami Daiji , Suzuki Daisuke , Tsuriya Daisuke , Machimura Hideo , Shimura Hidetoshi , Takeda Hiroshi , Yokomizo Hisashi , Takeshita Kei , Chin Keiichi , Kanasaki Keizo , Miyauchi Masaaki , Saburi Masuo , Morita Miwa , Yomota Miwako , Kimura Moritsugu , Hatori Nobuo , Nakajima Shinichi , Ito Shun , Tsukamoto Shunichiro , Murata Takashi , Matsushita Takaya , Furuki Takayuki , Hashimoto Takuya , Umezono Tomoya , Muta Yoshimi , Takashi Yuichi , Tamura Kouichi 
Published: December 2023

Aims Combination therapy with sodium-glucose cotransporter inhibitors (SGLT2is) and GLP-1 receptor agonists (GLP1Ras) is now of interest in clinical practice. The present study evaluated the effects of the preceding drug type on the renal outcome in clinical practice. Methods We retrospectively extracted type 2 diabetes mellitus patients who had received both SGLT2i and GLP1Ra treatment for at least 1 year. A total of 331 patients in the GLP1Ra-preceding group and 312 patients in the SGLT2i-preceding group were ultimately analyzed. Either progression of the albuminuria status and/or a ≥30% decrease in the eGFR was set as the primary renal composite outcome. The analysis using propensity score with inverse probability weighting was performed for the outcome. Results The incidences of the renal composite outcome in the SGLT2i- and GLP1Ra-preceding groups were 28% and 25%, respectively, with an odds ratio [95% confidence interval] of 1.14 [0.75, 1.73] ( p = .54). A logistic regression analysis showed that the mean arterial pressure (MAP) at baseline, the logarithmic value of the urine albumin-to-creatinine ratio at baseline, and the change in MAP were independent factors influencing the renal composite outcome. Conclusion With combination therapy of SGLT2i and GLP1Ra, the preceding drug did not affect the renal outcome.
Patient and Clinician Experiences With the Combination of Virtual and In-Person Chronic Kidney Disease Care Since the COVID-19 Pandemic
Authors: Bevilacqua Micheli , Melnyk Yuriy , Chiu Helen , Williams Janet , Watson Paul , Lee Brenda , Dhariwal Palvir , McGuire Marlee , Wei Julie , Chohan Robin , Logie Anne , Fryer Michele , Stoll Dominik , Levin Adeera 
Published: December 2023

Background: Following onset of the COVID-19 pandemic, chronic kidney disease (CKD) clinics in BC shifted from established methods of mostly in-person care delivery to virtual care (VC) and thereafter a hybrid of the two. Objectives: To determine strengths, weaknesses, quality-of-care delivery, and key considerations associated with VC usage to inform optimal way(s) of integrating virtual and traditional methods of care delivery in multidisciplinary kidney clinics. Design: Qualitative evaluation. Setting: British Columbia, Canada. Participants: Patients and health care providers associated with multidisciplinary kidney care clinics. Methods: Development and delivery of semi-structured interviews of patients and health care providers. Results: 11 patients and/or caregivers and 12 health care providers participated in the interviews. Participants reported mixed experiences with VC usage. All participants foresaw a future where both VC and in-person care was offered. A reported benefit of VC was convenience for patients. Challenges identified with VC included difficulty establishing new therapeutic relationships, and variable of abilities of both patients and health care providers to engage and communicate in a virtual format. Participants noted a preference for in-person care for more complex situations. Four themes were identified as considerations when selecting between in-person and VC: person’s nonmedical context, support available, clinical parameters and tasks to be completed, and clinic operations. Participants indicated that visit modality selection is an individualized and ongoing process involving the patient and their preferences which may change over time. Health care provider participants noted that new workflow challenges were created when using both VC and in-person care in the same clinic session. Limitations: Limited sample size in the setting of one-on-one interviews and use of convenience sampling which may result in missing perspectives, including those already facing challenges accessing care who could potentially be most disadvantaged by implementation of VC. Conclusions: A list of key considerations, aligned with quality care delivery was identified for health care providers and programs to consider as they continue to utilize VC and refine how best to use different visit modalities in different patient and clinical situations. Further work will be needed to validate these findings and evaluate clinical outcomes with the combination of virtual and traditional modes of care delivery. Trial registration: Not registered.
Outcomes of Lateral Meniscal Oblique Radial Tear Repair Compared With Intact Meniscus After ACL Reconstruction: A Cohort Study
Authors: Therrien Erik , Langhans Mark T. , Lamba Abhinav , Daniel Adam V. , Stuart Michael J. , Levy Bruce A. , Smith Patrick A. , Krych Aaron J. 
Published: December 2023

Background: Recently, the posterior horn lateral meniscal oblique radial tear (LMORT) was identified in 12% of acute anterior cruciate ligament (ACL) injuries. However, patient-reported outcomes for repair of this relatively common tear have not been reported. Purpose: To determine the minimum 2-year functional outcomes after LMORT repair at the time of ACL reconstruction (ACLR) compared to a matched cohort of patients who underwent isolated ACLR (iACLR). Study Design: Cohort study; Level of evidence, 3. Methods: Included were 100 patients (mean age at surgery, 21 years; range, 13-45 years) who underwent primary ACLR between 2010 and 2018. The mean follow-up period was 4.1 ± 2.0 years (range, 2.0-9.2 years). A total of 50 patients with surgically repaired LMORT type 3 or type 4 lesions, defined as partial or complete tears >10 mm from the root (LMORT group) were matched 1:1 based on age, date of surgery, and graft choice with 50 patients who underwent iACLR (iACLR group). The postoperative outcomes were compared between groups using the International Knee Documentation Committee subjective score (sIKDC) and the Tegner activity scale. An updated medical history was obtained via the electronic medical record to determine any subsequent complications and reoperations. Results: There was 1 ACL graft failure in each group as well as 5 (10%) reoperations per group. None of the patients in the LMORT group necessitated a lateral meniscal revision repair or partial meniscectomy. The LMORT and iACLR groups reported comparable sIKDC scores (92.5 ± 6.8 vs 91.9 ± 8.2, respectively; P = .712) as well as Tegner scores (6.7 ± 1.8 vs 6.6 ± 1.8, respectively; P = .910) at final follow-up. No failures of the LMORT repairs were reported. Conclusion: The study findings demonstrated that reoperations, graft failure rates, patient-reported outcomes, and patient activity levels at ≥2 years after type 3 and 4 LMORT repairs at the time of ACLR compared favorably with those of a matched cohort of patients who underwent iACLR with intact meniscus.
Hematopoietic and eosinophil-specific LNK(SH2B3) deficiency promotes eosinophilia and arterial thrombosis
Authors: Dou Huijuan , Wang Ranran , Tavallaie Mojdeh , Xiao Tong , Olszewska Malgorzata , Papapetrou Eirini P. , Tall Alan R. , Wang Nan 
Published: December 2023

Abstract
Increased eosinophil counts are associated with cardiovascular disease and may be an independent predictor of major cardiovascular events. However, the causality and underlying mechanisms are poorly understood. Genome-wide association studies have shown an association of a common LNK variant (R262W, T allele) with eosinophilia and atherothrombotic disorders. LNK(TT) reduces LNK function, and Lnk-deficient mice display accelerated atherosclerosis and thrombosis. This study was undertaken to assess the role of eosinophils in arterial thrombosis in mice with hematopoietic Lnk deficiency. Hematopoietic Lnk deficiency increased circulating and activated eosinophils, JAK/STAT signaling in eosinophils, and carotid arterial thrombosis with increased eosinophil abundance and extracellular trap formation (EETosis) in thrombi. Depletion of eosinophils by anti–Siglec-F antibody or by the ΔdbIGata1 mutation eliminated eosinophils in thrombi and markedly reduced thrombosis in mice with hematopoietic Lnk deficiency but not in control mice. Eosinophil depletion reduced neutrophil abundance and NETosis in thrombi without altering circulating neutrophil counts. To assess the role of Lnk specifically in eosinophils, we crossed Lnkf/f mice with eoCre mice. LnkΔeos mice displayed isolated eosinophilia, increased eosinophil activation, and accelerated arterial thrombosis associated with increased EETosis and NETosis in thrombi. DNase I infusion abolished EETs and neutrophil extracellular traps (NETs) in thrombi and reversed the accelerated thrombosis. Human induced pluripotent stem cell–derived LNK(TT) eosinophils showed increased activation and EETosis relative to isogenic LNK(CC) eosinophils, demonstrating human relevance. These studies show a direct link between eosinophilia, EETosis, and atherothrombosis in hematopoietic Lnk deficiency and an essential role of eosinophil LNK in suppression of arterial thrombosis.
Identification and surveillance of rare relapse-initiating stem cells during complete remission after transplantation
Authors: Dimitriou Marios , Mortera-Blanco Teresa , Tobiasson Magnus , Mazzi Stefania , Lehander Madeleine , Högstrand Kari , Karimi Mohsen , Walldin Gunilla , Jansson Monika , Vonlanthen Sofie , Ljungman Per , Langemeijer Saskia , Yoshizato Tetsuichi , Hellström-Lindberg Eva , Woll Petter S. , Jacobsen Sten Eirik W. 
Published: December 2023

Abstract
Relapse after complete remission (CR) remains the main cause of mortality after allogeneic stem cell transplantation for hematological malignancies and, therefore, improved biomarkers for early prediction of relapse remains a critical goal toward development and assessment of preemptive relapse treatment. Because the significance of cancer stem cells as a source of relapses remains unclear, we investigated whether mutational screening for persistence of rare cancer stem cells would enhance measurable residual disease (MRD) and early relapse prediction after transplantation. In a retrospective study of patients who relapsed and patients who achieved continuous-CR with myelodysplastic syndromes and related myeloid malignancies, combined flow cytometric cell sorting and mutational screening for persistence of rare relapse-initiating stem cells was performed in the bone marrow at multiple CR time points after transplantation. In 25 CR samples from 15 patients that later relapsed, only 9 samples were MRD-positive in mononuclear cells (MNCs) whereas flowcytometric-sorted hematopoietic stem and progenitor cells (HSPCs) were MRD-positive in all samples, and always with a higher variant allele frequency than in MNCs (mean, 97-fold). MRD-positivity in HSPCs preceded MNCs in multiple sequential samples, in some cases preceding relapse by &gt;2 years. In contrast, in 13 patients in long-term continuous-CR, HSPCs remained MRD-negative. Enhanced MRD sensitivity was also observed in total CD34+ cells, but HSPCs were always more clonally involved (mean, 8-fold). In conclusion, identification of relapse-initiating cancer stem cells and mutational MRD screening for their persistence consistently enhances MRD sensitivity and earlier prediction of relapse after allogeneic stem cell transplantation.
Performance analysis of conventional and AI-based variant callers using short and long reads
Authors: Abdelwahab Omar , Belzile François , Torkamaneh Davoud 
Published: December 2023

Abstract
Background
The accurate detection of variants is essential for genomics-based studies. Currently, there are various tools designed to detect genomic variants, however, it has always been a challenge to decide which tool to use, especially when various major genome projects have chosen to use different tools. Thus far, most of the existing tools were mainly developed to work on short-read data (i.e., Illumina); however, other sequencing technologies (e.g. PacBio, and Oxford Nanopore) have recently shown that they can also be used for variant calling. In addition, with the emergence of artificial intelligence (AI)-based variant calling tools, there is a pressing need to compare these tools in terms of efficiency, accuracy, computational power, and ease of use.

Results
In this study, we evaluated five of the most widely used conventional and AI-based variant calling tools (BCFTools, GATK4, Platypus, DNAscope, and DeepVariant) in terms of accuracy and computational cost using both short-read and long-read data derived from three different sequencing technologies (Illumina, PacBio HiFi, and ONT) for the same set of samples from the Genome In A Bottle project. The analysis showed that AI-based variant calling tools supersede conventional ones for calling SNVs and INDELs using both long and short reads in most aspects. In addition, we demonstrate the advantages and drawbacks of each tool while ranking them in each aspect of these comparisons.

Conclusion
This study provides best practices for variant calling using AI-based and conventional variant callers with different types of sequencing data.