bluuebunny/crossref_metadata_2025_split huggingface dataset:
BlockFusion: Expandable 3D Scene Generation using Latent Tri-plane Extrapolation
Authors: Wu Zhennan , Li Yang , Yan Han , Shang Taizhang , Sun Weixuan , Wang Senbo , Cui Ruikai , Liu Weizhe , Sato Hiroyuki , Li Hongdong , Ji Pan 
Published: July 2024

We present BlockFusion, a diffusion-based model that generates 3D scenes as unit blocks and seamlessly incorporates new blocks to extend the scene. BlockFusion is trained using datasets of 3D blocks that are randomly cropped from complete 3D scene meshes. Through per-block fitting, all training blocks are converted into the hybrid neural fields: with a tri-plane containing the geometry features, followed by a Multi-layer Perceptron (MLP) for decoding the signed distance values. A variational auto-encoder is employed to compress the tri-planes into the latent tri-plane space, on which the denoising diffusion process is performed. Diffusion applied to the latent representations allows for high-quality and diverse 3D scene generation.To expand a scene during generation, one needs only to append empty blocks to overlap with the current scene and extrapolate existing latent tri-planes to populate new blocks. The extrapolation is done by conditioning the generation process with the feature samples from the overlapping tri-planes during the denoising iterations. Latent tri-plane extrapolation produces semantically and geometrically meaningful transitions that harmoniously blend with the existing scene. A 2D layout conditioning mechanism is used to control the placement and arrangement of scene elements. Experimental results indicate that BlockFusion is capable of generating diverse, geometrically consistent and unbounded large 3D scenes with unprecedented high-quality shapes in both indoor and outdoor scenarios.
BRCA Status Dictates Wnt Responsiveness in Epithelial Ovarian Cancer
Authors: Chehade Hussein , Gogoi Radhika , Adzibolosu Nicholas K. , Galoforo Sandra , Fehmi Rouba-Ali , Kheil Mira , Fox Alexandra , Kim Seongho , Rattan Ramandeep , Hou Zhanjun , Morris Robert T. , Matherly Larry H. , Mor Gil , Alvero Ayesha B. 
Published: July 2024

Abstract

The association of BRCA1 and BRCA2 mutations with increased risk for developing epithelial ovarian cancer is well established. However, the observed clinical differences, particularly the improved therapy response and patient survival in BRCA2-mutant patients, are unexplained. Our objective is to identify molecular pathways that are differentially regulated upon the loss of BRCA1 and BRCA2 functions in ovarian cancer. Transcriptomic and pathway analyses comparing BRCA1-mutant, BRCA2-mutant, and homologous recombination wild-type ovarian tumors showed differential regulation of the Wnt/β-catenin pathway. Using Wnt3A-treated BRCA1/2 wild-type, BRCA1-null, and BRCA2-null mouse ovarian cancer cells, we observed preferential activation of canonical Wnt/β-catenin signaling in BRCA1/2 wild-type ovarian cancer cells, whereas noncanonical Wnt/β-catenin signaling was preferentially activated in the BRCA1-null ovarian cancer cells. Interestingly, BRCA2-null mouse ovarian cancer cells demonstrated a unique response to Wnt3A with the preferential upregulation of the Wnt signaling inhibitor Axin2. In addition, decreased phosphorylation and enhanced stability of β-catenin were observed in BRCA2-null mouse ovarian cancer cells, which correlated with increased inhibitory phosphorylation on GSK3β. These findings open venues for the translation of these molecular observations into modalities that can impact patient survival.

Significance:
We show that BRCA1 and BRCA2 mutation statuses differentially impact the regulation of the Wnt/β-catenin signaling pathway, a major effector of cancer initiation and progression. Our findings provide a better understanding of molecular mechanisms that promote the known differential clinical profile in these patient populations.
Effect of Intramyocardial Administration of Baculovirus Encoding the Transcription Factor Tbx20 in Sheep With Experimental Acute Myocardial Infarction
Authors: Bauzá María del Rosario , López Ayelén Emilce , Simonin Jorge Alejandro , Cimbaro Francisco Stefano , Scharn Agustina , Castro Araceli , Silvestro Cintia Virginia , Cuniberti Luis Alberto , Crottogini Alberto José , Belaich Mariano Nicolás , Locatelli Paola , Olea Fernanda Daniela 
Published: July 2024

Background

Gene therapy has been proposed as a strategy to induce cardiac regeneration following acute myocardial infarction (AMI). Given that Tbx20, a transcription factor of the T‐box subfamily, stimulates cell proliferation and angiogenesis, we designed a baculovirus overexpressing
Tbx20
(Bv‐Tbx20) and evaluated its effects in cultured cardiomyocytes and in an ovine model of AMI.

Methods and Results

Cell proliferation and angiogenesis were measured in cardiomyocytes transduced with Bv‐Tbx20 or Bv‐Null (control). Subsequently, in sheep with AMI, Bv‐Tbx20 or Bv‐Null was injected in the infarct border. Cardiomyocyte cell cycle activity, angioarteriogenesis, left ventricular function, and infarct size were assessed. Cardiomyocytes transduced with BvTbx20 increased cell proliferation, cell cycle regulatory and angiogenic gene expression, and tubulogenesis. At 7 days posttreatment, sheep treated with Bv‐Tbx20 showed increased
Tbx20
, promitotic and angiogenic gene expression, decreased levels of
P21
, increased Ki67‐ (17.09±5.73 versus 7.77±7.24 cardiomyocytes/mm
2
,
P
<0.05) and PHH3 (phospho‐histone H3)‐labeled cardiomyocytes (10.10±3.51 versus 5.23±2.87 cardiomyocytes/mm
2
,
P
<0.05), and increased capillary (2302.68±353.58 versus 1694.52±211.36 capillaries/mm
2
,
P
<0.001) and arteriolar (146.95±53.14 versus 84.06±16.84 arterioles/mm
2
,
P
<0.05) densities. At 30 days, Bv‐Tbx20 decreased infarct size (9.89±1.92% versus 12.62±1.33%,
P
<0.05) and slightly improved left ventricular function. Baculoviral gene transfer‐mediated Tbx20 overexpression exerted angiogenic and cardiomyogenic effects in vitro.

Conclusions
In sheep with AMI, Bv‐Tbx20 induced angioarteriogenesis, cardiomyocyte cell cycle activity, infarct size limitation, and a slight recovery of left ventricular function, suggesting that Bv‐Tbx20 gene therapy may contribute to cardiac regeneration following AMI.
Extracellular RNA Induces Neutrophil Recruitment Via Toll‐Like Receptor 3 During Venous Thrombosis After Vascular Injury
Authors: Najem Maria Y. , Rys Ryan N. , Laurance Sandrine , Bertin François‐René , Gourdou‐Latyszenok Virginie , Gourhant Lénaïck , Le Gall Lauriane , Le Corre Rozenn , Couturaud Francis , Blostein Mark D. , Lemarié Catherine A. 
Published: July 2024

Background
Venous thromboembolism is associated with endothelial cell activation that contributes to the inflammation‐dependent activation of the coagulation system. Cellular damage is associated with the release of different species of extracellular RNA (eRNA) involved in inflammation and coagulation. TLR3 (toll‐like receptor 3), which recognizes (viral) single‐stranded or double‐stranded RNAs and self‐RNA fragments, might be the receptor of these species of eRNA during venous thromboembolism. Here, we investigate how the TLR3/eRNA axis contributes to venous thromboembolism.

Methods and Results

Thrombus formation and size in wild‐type and TLR3 deficient (−/−) mice were monitored by ultrasonography after venous thrombosis induction using the ferric chloride and stasis models. Mice were treated with RNase I, with polyinosinic‐polycytidylic acid, a TLR3 agonist, or with RNA extracted from murine endothelial cells. Gene expression and signaling pathway activation were analyzed in HEK293T cells overexpressing TLR3 in response to eRNA or in human umbilical vein endothelial cells transfected with a small interference RNA against TLR3. Plasma clot formation on treated human umbilical vein endothelial cells was analyzed. Thrombosis exacerbated eRNA release in vivo and increased eRNA content within the thrombus. RNase I treatment reduced thrombus size compared with vehicle‐treated mice (
P
<0.05). Polyinosinic‐polycytidylic acid and eRNA treatments increased thrombus size in wild‐type mice (
P
<0.01 and
P
<0.05), but not in TLR3
−/−
mice, by reinforcing neutrophil recruitment (
P
<0.05). Mechanistically, TLR3 activation in endothelial cells promotes CXCL5 (C‐X‐C motif chemokine 5) secretion (
P
<0.001) and NFκB (nuclear factor kappa‐light‐chain‐enhancer of activated B cells) activation (
P
<0.05). Finally, eRNA triggered plasma clot formation in vitro (
P
<0.01).

Conclusions
We show that eRNA and TLR3 activation enhance venous thromboembolism through neutrophil recruitment possibly through secretion of CXCL5, a potent neutrophil chemoattractant.
Deconstructing the Mapper algorithm to extract richer topological and temporal features from functional neuroimaging data
Authors: Haşegan Daniel , Geniesse Caleb , Chowdhury Samir , Saggar Manish 
Published: July 2024

Abstract
Capturing and tracking large-scale brain activity dynamics holds the potential to deepen our understanding of cognition. Previously, tools from topological data analysis, especially Mapper, have been successfully used to mine brain activity dynamics at the highest spatiotemporal resolutions. Even though it is a relatively established tool within the field of topological data analysis, Mapper results are highly impacted by parameter selection. Given that noninvasive human neuroimaging data (e.g., from fMRI) is typically fraught with artifacts and no gold standards exist regarding “true” state transitions, we argue for a thorough examination of Mapper parameter choices to better reveal their impact. Using synthetic data (with known transition structure) and real fMRI data, we explore a variety of parameter choices for each Mapper step, thereby providing guidance and heuristics for the field. We also release our parameter exploration toolbox as a software package to make it easier for scientists to investigate and apply Mapper to any dataset.
Transient destabilization of interhemispheric functional connectivity induced by spreading depolarization
Authors: Lachinova Daria A. , Smirnova Maria P. , Pavlova Irina V. , Sysoev Ilya V. , Vinogradova Lyudmila V. 
Published: July 2024

Abstract
Cortical spreading depolarization (CSD), a slowly propagating wave of transient cellular depolarization, is a reliable cortical response to various brain insults (stroke, trauma, seizures) and underlying mechanism of migraine aura. Little is known about CSD effects on brain network activity. Using undirected (mutual information, MI) and directed (transfer entropy, TE) measures, we studied the dynamics of cross-hemispheric connectivity associated with the development of unilateral CSD in freely behaving rats and the involvement of inhibitory transmission in mechanisms of the coupling changes. We show that the development of CSD in the cortex of one hemisphere is followed by the transient loss of undirected functional connectivity (MI) between ipsilateral and contralateral cortical regions. The post-CSD functional disconnection of the hemispheres was accompanied by an increase in driving force from an unaffected contralateral cortex to an affected one (TE). Mild cortical disinhibition produced by pretreatment with an inhibitory receptor blocking agent (penthylenetetrazole) did not affect CSD but attenuated (MI) or eliminated (TE) the CSD-induced connectivity changes. The effects of CSD on functional connectivity in awake rodents were similar at the individual and group levels, suggesting that the described connectivity response may be a promising network biomarker of CSD occurrence in patients.
Outcomes of patients with R/R B-cell NHL and limited (&lt;5 sites) pre-CART disease bridged with or without radiotherapy
Authors: Saifi Omran , Breen William G. , Lester Scott C. , Rule William G. , Stish Bradley J. , Rosenthal Allison , Munoz Javier , Lin Yi , Bansal Radhika , Hathcock Matthew A. , Johnston Patrick B. , Ansell Stephen M. , Paludo Jonas , Khurana Arushi , Villasboas Jose C. , Wang Yucai , Iqbal Madiha , Alhaj Moustafa Muhamad , Murthy Hemant S. , Ayala Ernesto , Kharfan-Dabaja Mohamed A. , Hoppe Bradford S. , Peterson Jennifer L. 
Published: July 2024

Abstract
Unirradiated patients with relapsed/refractory (R/R) B-cell non-Hodgkin lymphoma (NHL) who undergo anti-CD19 chimeric antigen receptor T-cell therapy (CART) have a predominant localized pattern of relapse, the significance of which is heightened in individuals with limited/localized disease before CART. This study reports on the outcomes of patients with R/R NHL and limited (&lt;5 involved sites) disease bridged with or without radiotherapy. A multicenter retrospective review of 150 patients with R/R NHL who received CART with &lt;5 disease sites before leukapheresis was performed. Bridging treatment, if any, was administered between leukapheresis and CART infusion. Study end points included relapse-free survival (RFS), event-free survival (EFS), and overall survival. Before CART infusion, 48 patients (32%) received bridging radiotherapy (BRT), and 102 (68%) did not. The median follow-up was 21 months. After CART infusion, BRT patients had higher objective response (92% vs 78%; P = .046) and sustained complete response rates (54% vs 33%; P = .015). Local relapse in sites present before CART was lower in the BRT group (21% vs 46%; P = .003). BRT patients had improved 2-year RFS (53% vs 44%; P = .023) and 2-year EFS (37% vs 34%; P = .039) compared with patients who did not receive BRT. The impact of BRT was most prominent in patients who had ≤2 pre-CART involved disease sites, with 2-year RFS of 62% in patients who received BRT compared with 42% in those who did not (P = .002). BRT before CART for patients with limited (&lt;5 involved disease sites) R/R NHL improves response rate, local control, RFS, and EFS without causing significant toxicities.
Some virulence genes are associated with antibiotic susceptibility in Enterobacter cloacae complex
Authors: Mosaffa Fatemeh , Saffari Fereshteh , Veisi Mahin , Tadjrobehkar Omid 
Published: July 2024

Abstract
Background
Enterobacter cloacae complex (ECC) including different species are isolated from different human clinical samples. ECC is armed by many different virulence genes (VGs) and they were also classified among ESKAPE group by WHO recently. The present study was designed to find probable association between VGs and antibiotic susceptibility in different ECC species.

Methods
Forty-five Enterobacter isolates that were harvested from different clinical samples were classified in four different species. Seven VGs were screened by PCR technique and antibiotic susceptibility assessment was performed by disk-diffusion assay.

Result
Four Enterobacter species; Enterobacter cloacae (33.3%), Enterobacter hormaechei (55.6%), Enterobacter kobei (6.7%) and Enterobacter roggenkampii (4.4%) were detected. Minimum antibiotic resistance was against carbapenem agents and amikacin even in MDR isolates. 33.3% and 13.3% of isolates were MDR and XDR respectively. The rpoS (97.8%) and csgD (11.1%) showed maximum and minimum frequency respectively. Blood sample isolated were highly virulent but less resistant in comparison to the other sample isolates. The csgA, csgD and iutA genes were associated with cefepime sensitivity.

Conclusion
The fepA showed a predictory role for differentiating of E. hormaechei from other species. More evolved iron acquisition system in E. hormaechei was hypothesized. The fepA gene introduced as a suitable target for designing novel anti-virulence/antibiotic agents against E. hormaechei. Complementary studies on other VGs and ARGs and with bigger study population is recommended.
Comprehensive analysis of PHF5A as a potential prognostic biomarker and therapeutic target across cancers and in hepatocellular carcinoma
Authors: Cheng Qianqian , Ji Wenbin , Lv Zhenyu , Wang Wei , Xu Zhaiyue , Chen Shaohua , Zhang Wenting , Shao Yu , Liu Jing , Yang Yan 
Published: July 2024

Abstract
Objective
Cancer is a predominant cause of death globally. PHD-finger domain protein 5 A (PHF5A) has been reported to participate in various cancers; however, there has been no pan-cancer analysis of PHF5A. This study aims to present a novel prognostic biomarker and therapeutic target for cancer treatment.

Methods
This study explored PHF5A expression and its impact on prognosis, tumor mutation burden (TMB), microsatellite instability (MSI), functional status and tumor immunity across cancers using various public databases, and validated PHF5A expression and its correlation with survival, immune evasion, angiogenesis, and treatment response in hepatocellular carcinoma (HCC) using bioinformatics tools, qRT-PCR and immunohistochemistry (IHC).

Results
PHF5A was differentially expressed between tumor and corresponding normal tissues and was correlated with prognosis in diverse cancers. Its expression was also associated with TMB, MSI, functional status, tumor microenvironment, immune infiltration, immune checkpoint genes and tumor immune dysfunction and exclusion (TIDE) score in diverse malignancies. In HCC, PHF5A was confirmed to be upregulated by qRT-PCR and IHC, and elevated PHF5A expression may promote immune evasion and angiogenesis in HCC. Additionally, multiple canonical pathways were revealed to be involved in the biological activity of PHF5A in HCC. Moreover, immunotherapy and transcatheter arterial chemoembolization (TACE) worked better in the low PHF5A expression group, while sorafenib, chemotherapy and AKT inhibitor were more effective in the high expression group.

Conclusions
This study provides a comprehensive understanding of the biological function of PHF5A in the carcinogenesis and progression of various cancers. PHF5A could serve as a tumor biomarker related to prognosis across cancers, especially HCC, and shed new light on the development of novel therapeutic targets.
Phenotypic characteristics and rehabilitation effect of children with regressive autism spectrum disorder: a prospective cohort study
Authors: Hu Chaoqun , Yang Ting , Chen Jie , Dai Ying , Wei Hua , Wu Qionghui , Chen Hongyu , Long Dan , Feng Yuru , Wei Qiuhong , Zhang Qian , Chen Li , Li Tingyu 
Published: July 2024

Abstract
Background
In this prospective cohort study, we determined the phenotypic characteristics of children with regressive autism spectrum disorder (ASD) and explored the effects of rehabilitation.

Methods
We recruited 370 children with ASD aged 1.5–7 years. Based on the Regression Supplement Form, the children were assigned to two groups: regressive and non-regressive. The core symptoms and neurodevelopmental levels of ASD were assessed before and after 1 year of behavioral intervention using the Autism Diagnostic Observation Schedule (ADOS), Social Response Scale (SRS), Children Autism Rating Scale (CARS), and Gesell Developmental Scale (GDS).

Results
Among the 370 children with ASD, 28.38% (105/370) experienced regression. Regression was primarily observed in social communication and language skills. Children with regressive ASD exhibited higher SRS and CARS scores and lower GDS scores than those with non-regressive ASD. After 1 year of behavioral intervention, the symptom scale scores significantly decreased for all children with ASD; however, a lesser degree of improvement was observed in children with regressive ASD than in those with non-regressive ASD. In addition, the symptom scores of children with regressive ASD below 4 years old significantly decreased, whereas the scores of those over 4 years old did not significantly improve. Children with regressive ASD showed higher core symptom scores and lower neurodevelopmental levels. Nevertheless, after behavioral intervention, some symptoms exhibited significant improvements in children with regressive ASD under 4 years of age.

Conclusion
Early intervention should be considered for children with ASD, particularly for those with regressive ASD.
“We chose PrEP because I wanted to be sure that this child my wife was going to conceive was indeed mine.” Factors influencing the choice of safer conception methods and experiences with its use: a qualitative study among HIV sero-discordant couples in Zimbabwe
Authors: Brown Joelle M. , Musara Petina , Gitome Serah , Chitukuta Miria , Mataveke Bismark , Chirenda Thandiwe , Mgodi Nyaradzo , Mutero Prisca , Matubu Allen , Chareka Gift , Chasakara Charles , Murombedzi Caroline , Makurumure Tinei , Hughes Carolyn Smith , Bukusi Elizabeth , Cohen Craig R. , Shiboski Stephen , Darbes Lynae , Rutherford George W. , Chirenje Z. Michael , Mhlanga Felix 
Published: July 2024

Abstract
Background
Safer conception services are needed to minimize HIV transmission among HIV sero-discordant couples desiring pregnancy. Few studies have evaluated the choices couples make when they are offered multiple safer conception methods or real-world method acceptability. This paper addresses an important knowledge gap regarding factors that influence the choice of safer conception methods, couples' actual experiences using safer conception methods, and why some couples switch safer conception methods.

Methods
Between February and June 2019, we conducted semi-structured in-depth interviews among 14 men and 17 women, representing 17 couples who exited the SAFER study—a pilot safer conception study for HIV sero-discordant couples in Zimbabwe that offered couples a choice of ART with monthly viral load monitoring (ART/VL), oral PrEP, vaginal insemination, and semen washing. All couples in SAFER had used at least two safer conception methods.

Results
We found that safer conception method choice often centered around a desire for intimacy, condomless sex, and certainty in the conception process, particularly for men. Method-related attributes such as familiarity, perceived ease of use, side effects, and perceived level of effectiveness in preventing HIV and achieving pregnancy influenced method choice, switching, and satisfaction. Concerns were expressed about each safer conception method and couples were willing to try different methods until they found method(s) that worked for them. The majority of participants reported having positive experiences using safer conception, especially those using ART/VL + PrEP, citing that they were able to attempt pregnancy for the first time with peace of mind and experienced joy and satisfaction from being able to achieve pregnancy safely.

Conclusions
The differences in method preferences and experiences voiced by participants in this study and in other studies from the region point to the importance of having a variety of safer conception options in the service delivery package and addressing concerns about paternity, intimacy, and method-related attributes to enable HIV sero-discordant couples to safely achieve their reproductive goals.