bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tunable capacitor for superconducting qubits using an InAs/InGaAs heterostructure
Authors: Materise Nicholas , Dartiailh Matthieu C , Strickland William M , Shabani Javad , Kapit Eliot 
Published: July 2023

Abstract
Adoption of fast, parametric coupling elements has improved the performance of superconducting qubits, enabling recent demonstrations of quantum advantage in randomized sampling problems. The development of low loss, high contrast couplers is critical for scaling up these systems. We present a blueprint for a gate-tunable coupler realized with a two-dimensional electron gas in an InAs/InGaAs heterostructure. Rigorous numerical simulations of the semiconductor and high frequency electromagnetic behavior of the coupler and microwave circuitry yield an on/off ratio of more than one order of magnitude. We give an estimate of the dielectric-limited loss from the inclusion of the coupler in a two qubit system, with coupler coherences ranging from a few to tens of microseconds.
Lessons from 801 clinical TFE3/TFEB fluorescence in situ hybridization assays performed on renal cell carcinoma suspicious for MiTF family aberrations
Authors: Wang Xiao-Ming , Shao Lina , Xiao Hong , Myers Jeffrey L , Pantanowitz Liron , Skala Stephanie L , Udager Aaron M , Vaishampayan Ulka , Mannan Rahul , Dhanasekaran Saravana M , Chinnaiyan Arul M , Betz Bryan L , Brown Noah , Mehra Rohit 
Published: July 2023

Abstract

Objectives
Fluorescence in situ hybridization (FISH) assays for the detection of chromosomal rearrangements involving TFE3 and TFEB are considered the gold standard for the diagnosis of MiTF family altered renal cell carcinoma (MiTF-RCC). We reviewed 801 clinical TFE3/TFEB FISH assays performed at our tertiary-level institution between 2014 and 2023 on kidney tumors suspicious at the morphologic or biomarker level for MiTF aberrations.

Methods
We summarized and analyzed clinical information, TFE3/TFEB FISH results, and available biomarker staining results in a cohort of 453 consecutive kidney tumor cases suspicious for MiTF-RCC.

Results
In total, 61 of 434 (14%) kidney tumors were confirmed for TFE3 translocation; 10 of 367 cases (2.7%) were confirmed for TFEB translocation. Since TFEB amplification interpretation was implemented in our service line, 20 of 306 cases (6.5%) were diagnosed with TFEB amplification. Importantly, TFE3 and TFEB rearrangements were never co-detected within the same kidney tumor. Patients with TFEB amplification were significantly older (P &lt; .001) than patients with TFE3 or TFEB translocation. Kidney tumors with TFEB amplification were seen to be at least 3 times as common as those with TFEB translocation.

Conclusions
Clinical TFE3/TFEB FISH assays successfully identified and confirmed rare MiTF-RCC with TFE3 and TFEB rearrangements. Although morphologic and biomarker features associated with a kidney tumor may be suggestive of MiTF-RCC, clinical TFE3/TFEB FISH assays are crucial for a confirmation and definitive subclassification of patients with MiTF-RCC.
A soft-computation hybrid method for search of the antibiotic-resistant gene in Mycobacterium tuberculosis for promising drug target identification and antimycobacterial lead discovery
Authors: Jaiswal Neha , Kumar Awanish 
Published: July 2023

Summary
Tuberculosis (TB) control programs were already piloted before the COVID-19 pandemic commenced and the global TB response was amplified by the pandemic. To combat the global TB epidemic, drug repurposing, novel drug discovery, identification and targeting of the antimicrobial resistance (AMR) genes, and addressing social determinants of TB are required. The study aimed to identify AMR genes in Mycobacterium tuberculosis (MTB) and a new anti-mycobacterial drug candidate. In this research, we used a few software to explore some AMR genes as a target protein in MTB and identified some potent antimycobacterial agents. We used Maestro v12.8 software, along with STRING v11.0, KEGG and Pass Server databases to gain a deeper understanding of MTB AMR genes as drug targets. Computer-aided analysis was used to identify mtrA and katG AMR genes as potential drug targets to depict some antimycobacterial drug candidates. Based on docking scores of –4.218 and –6.161, carvacrol was identified as a potent inhibitor against both drug targets. This research offers drug target identification and discovery of antimycobacterial leads, a unique and promising approach to combating the challenge of antibiotic resistance in Mycobacterium, and contributes to the development of a potential futuristic solution.
Vascular complications of ProGlide versus Prostar in transcatheter aortic valve replacement (TAVR) procedures: meta-analysis
Authors: Xiang Yuwei , Chen Chen , Zhao Jichun , Ma Yukui , Huang Bin , Wu Zhoupeng 
Published: July 2023

Abstract

Background
The aim of this study was to compare the vascular complications of ProGlide and Prostar in percutaneous transfemoral transcatheter aortic valve replacement.

Methods
Electronic databases were searched in July 2022 for studies that compared the vascular complications of ProGlide and Prostar for percutaneous closure in transcatheter aortic valve replacement. The primary outcome was major vascular complications and the secondary outcomes were minor vascular complications, types of access-site vascular complications, device failure, and additional intervention. Estimates of relative effects were pooled to generate ORs and their 95 per cent c.i. using a random-effects model. The risk of bias in non-randomized comparative studies was assessed using the Risk Of Bias In Non-randomized Studies - of Interventions (‘ROBINS-I’) tool.

Results
Nine studies were identified and a total of 7529 patients were included. Among them, 4144 patients received ProGlide and 3385 received Prostar. The pooled data showed that the risk of major vascular complications was significantly lower with ProGlide versus Prostar (OR 0.50, 95 per cent c.i. 0.32 to 0.78). Regarding the types of vascular complications, vascular trauma was the most common complication and the risk was similar between groups (OR 1.02, 95 per cent c.i. 0.55 to 1.91). ProGlide had a lower risk of bleeding complications (OR 0.46, 95 per cent c.i. 0.22 to 0.94), but a higher risk of ischaemia complications (OR 1.90, 95 per cent c.i. 1.10 to 3.27). The risk of device failure was lower in the ProGlide group (OR 0.45, 95 per cent c.i. 0.21 to 0.95). Both groups had a similar risk of having additional interventions for vascular complications (OR 1.02, 95 per cent c.i. 0.75 to 1.39). The use of ProGlide was associated with a lower risk of additional surgical treatments (OR 0.52, 95 per cent c.i. 0.34 to 0.80), but a higher risk of endovascular treatments (OR 2.69, 95 per cent c.i. 1.29 to 5.63).

Conclusion
In percutaneous transfemoral transcatheter aortic valve replacement procedures, ProGlide has superior safety and efficacy when compared with Prostar; it is associated with fewer major vascular complications and device failures. The vascular complications of ProGlide are more likely to be dealt with using endovascular treatments than surgical treatments.
A Masking Effect: A Case of Initial Presentation of Ulcerative Colitis After Discontinuing Growth Hormone Therapy
Authors: Ugonabo Onyinye , Turki M'hamed , Stewart Dane , Sherif Ahmed , Villa Xavier 
Published: July 2023

AbstractBackgroundThe inflammation and repair of the intestinal mucosa in inflammatory bowel disease (IBD) involve a complex interplay between innate, adaptive immune responses, and hormones. This may explain the relapsing clinical course of the disease.MethodsWe present the first reported case of a patient presenting their initial flare of ulcerative colitis immediately after discontinuing growth hormone (GH) therapy, suggesting treatment with GH or growth factors may prevent the development of IBD.ResultsThis is a case of a 13-year-old female with a history of GH deficiency, presenting with an 8-week history of abdominal pain, blood-stained diarrhea, and fecal calprotectin greater than 8000 mcg/g, 2 weeks after discontinuing GH therapy. The patient subsequently underwent an esophagoduodenoscopy and colonoscopy with biopsies showing histological features consistent with ulcerative colitis.ConclusionsThe finding of withdrawing GH or growth factors therapy potentially unmasking IBD in this patient raises a question of whether growth factors can inhibit the development of IBD and suggests beneficial effects of treatment with GH or growth factors as adjuvant therapy for IBD.
Impacts of brood parasitism by shiny cowbird Molothrus bonariensis on the breeding success of a small host, the black-backed water tyrant Fluvicola albiventer
Authors: Vanesa Sovrano Lorena , Jesica León Evelina , Ezequiel Lorenzón Rodrigo , Fernanda Olguín Pamela , Héctor Beltzer Adolfo , Raúl Giraudo Alejandro 
Published: July 2023

Abstract
The shiny cowbird Molothrus bonariensis parasitizes many species with different life-history traits and has a detrimental effect on the survival of the progeny of the hosts. In response, hosts have developed numerous antiparasitic defenses. Here, we examined the effects of brood parasitism by shiny cowbird on the clutch and brood sizes (83 nests) in a small host, the black-backed water tyrant Fluvicola albiventer. We also studied whether the death of parasite nestlings was related to the care of the foster parents and whether the host had any antiparasitic defense against the shiny cowbird. Our results indicate that brood parasitism significantly decreased the host hatching and fledging successes. The majority of nest failures (57%) were caused by brood parasitism. Shiny cowbird parasitism occurred in 52% of nests and the intensity of parasitism was 1.23 ± 0.53 eggs per parasitized nest. Of the total host eggs, 54% were damaged. During the incubation stage, 20 nests (47%) were abandoned because of egg punctures by shiny cowbirds females. Only two parasitic fledglings were recorded, while the remaining nestlings either died from starvation (n = 12) or predation (n = 3). Foster parents abandoned parasitic nestlings between 5 and 10 days old. Our findings demonstrate that the shiny cowbird has very low rates of fledging success when parasitizing black-backed water tyrant. Also, parasitism had a high reproductive cost in the black-backed water tyrant because a very low proportion (7%) of the parasitized nests (n = 43) were successful.
A case report of high-output heart failure due to arteriovenous shunt without bowel: how to address?
Authors: Habibi Zarina , Abma-Kramer Johanna , Brunner-La Rocca Hans-Peter 
Published: July 2023

Abstract

Background
High-output heart failure (HF) is a form of HF where patients present with a high-output state with low systemic vascular resistance. This report presents the case of high-output HF in a patient with an arteriovenous shunt and no options for oral-administered drugs.

Case summary
A 70-year-old male with a terminal jejunostomy fully depending on parenteral feeding through a vena saphena magna shunt presented with symptoms of shortness of breath. Echocardiography revealed eccentric hypertrophy with reduced left ventricular ejection fraction (LVEF) and atrial fibrillation with a heart rate of 70–100 b.p.m. Cardiac magnetic resonance imaging, endomyocardial biopsy, and cardiomyopathy lab revealed no cause of HF. High-output HF based on right heart catheterization due to the arteriovenous shunt or related to irregularity due to atrial fibrillation were potential causes. As a result of his malfunctioning gastrointestinal system, the pharmacological options were limited. He was treated with captopril sublingual, initially 6.25 mg three times daily (TID) and later 12.5 mg TID, which reduced blood pressure. Electrical cardioversion to sinus rhythm was successful but did not improve LVEF. Therefore, the patient was opted for surgically reducing the blood flow through the shunt, resulting in normalization of LVEF.

Discussion
High-output HF is an uncommon form of HF with an uncertain prevalence. The most common aetiologies reported in the literature are obesity, cirrhosis, and arteriovenous shunts. Sublingual administration of captopril can be an effective treatment option for HF patients unable to absorb oral-administered drugs.
Investigating Heterogeneity in the Relationship Between Marital Satisfaction and Cognitive Health by Gender and Across the Cognitive Function Distribution
Authors: Kim Jinho , Kwon Keun Young 
Published: July 2023

Abstract

Background and Objectives
Marital satisfaction has been established as an essential factor for promoting health and well-being in older adults. However, it is unclear whether marital satisfaction is also associated with cognitive health in this population. This study aimed to investigate the longitudinal association between marital satisfaction and cognitive function, while also exploring variations in this relationship by gender and across the cognitive function distribution.

Research Design and Methods
This study used 6 waves of the Korean Longitudinal Study of Ageing (KLoSA) and employed gender-stratified unconditional quantile regression (UQR) models with fixed effects (FE) to estimate the association between marital satisfaction and cognitive function across different quantiles of the cognitive function distribution. FE models controlled for unobserved individual-level confounders such as genetics, cognitive and noncognitive skills, and early childhood social and cultural background.

Results
The results of this study revealed that marital satisfaction was positively associated with cognitive function (b = 0.305), and this association was stronger in older men than in older women (b = 0.392 for older men vs b = 0.181 for older women). The UQR-FE models suggested that stronger association between marital satisfaction and cognitive function was observed among older men with lower cognitive function (b = 0.817 for 10th percentile vs b = 0.118 for 90th percentile). Among older women, no clear patterns of heterogeneity were found across the cognitive function distribution.

Discussion and Implications
The findings of this study highlight a significant degree of heterogeneity in the relationship between marital satisfaction and cognitive function among older men, with stronger associations observed in the lower percentiles of the cognitive function distribution. Interventions aimed at improving marital quality could be an effective strategy for promoting cognitive health in older adults, with an approach tailored to the individual’s characteristics.
Position Statement of the Max Planck Institute for Innovation and Competition of 2 May 2023 on the Implementation of the Digital Markets Act (DMA)
Authors: Drexl Josef , Conde Gallego Beatriz , González Otero Begoña , Herrmann Liza , Hoffmann Jörg , Johannsen Germán Oscar , Kestler Lukas , Matarazzi Giulio 
Published: July 2023

Abstract
The Max Planck Institute for Innovation and Competition is a research institute within the Max Planck Society for the Advancement of Science. The Institute is committed to fundamental legal and economic research on processes of innovation and competition and their regulation. Its research focus is on the incentives, determinants and implications of innovation. The Institute informs and guides legal and economic discourse on an impartial basis. It hereby provides its position on the implementation of Regulation (EU) 2022/1925 of the European Parliament and of the Council of 14 September 2022 on contestable and fair markets in the digital sector and amending Directives (EU) 2019/1937 and (EU) 2020/1828 (Digital Markets Act; DMA).
A novel antisense lncRNA, ARBAG harboring an RNA destabilizing GWAS variant for C-peptide dictates the transcript isoforms of GABRA6 in cerebellum
Authors: Bandesh Khushdeep , Pal Muneesh , Balakrishnan Abitha , Gautam Pradeep , Jha Punam , Tandon Nikhil , Pillai Beena , Bharadwaj Dwaipayan 
Published: July 2023

Abstract
Human disease-associated genetic variations often map to long non-coding RNA (lncRNA) genes; however, elucidation of their functional impact is challenging. We previously identified a new genetic variant rs4454083 (A/G) residing in exon of an uncharacterized lncRNA ARBAG that strongly associates with plasma levels of C-peptide, a hormone that regulates insulin bioavailability. On the opposite strand, rs4454083 also corresponds to an intron of a cerebellum-specific GABA receptor subunit gene GABRA6 that mediates strengthening of inhibitory synapses by insulin. Here, we show that alleles of rs4454083 modulate transcript levels of the antisense gene, ARBAG, which then controls the expression of the sense gene, GABRA6. Predisposing to low C-peptide, GG (a minor allele genotype across ethnicities) stabilizes ARBAG lncRNA causing higher transcript levels in cerebellum. ARBAG lncRNA abundance leads to cleavage of GABRA6 mRNA at the complementary region, resulting in a dysfunctional GABRA6 protein that would not be recruited for synapse strengthening. Together, our findings in human cerebellar cell-line and induced Pluripotent Stem Cells (iPSCs) demonstrate biological role of a novel lncRNA in determining the ratio of mRNA isoforms of a protein-coding gene and the ability of an embedded variant in modulating lncRNA stability leading to inter-individual differences in protein expression.
Detection of Human Papillomavirus DNA, E6/E7 Messenger RNA, and p16INK4a in Lung Cancer: A Systematic Review and Meta-analysis
Authors: Li Xiaoxuan , Ling Yihong , Hu Lina , Zhang Lihong , Lin Suxia , Zhang Xuanye , Zang Shengbing 
Published: July 2023

Abstract

Background
The etiologic link between human papillomavirus (HPV) and lung cancer is still controversial.

Methods
PubMed and Cochrane databases were searched from inception to December 2020 to identify studies on the infection of HPV in lung cancer. We calculated the attributable proportion of HPV in lung cancer by pooling the infection of cases positive for both HPV DNA and biomarkers of carcinogenesis that may be induced by HPV (E6/E7 messenger RNA or p16INK4a).

Results
A total of 117 studies, comprising data of 12 616 lung cancer cases from 22 countries across 5 continents, were included. The overall HPV DNA positivity in primary lung cancer cases worldwide was 16.4% (95% confidence interval, 12.7%–20.5%). HPV DNA positivity of lung cancer varied significantly by pathological type and geographic region. Notably, the expression rate of p16INK4a is significantly higher than the positivity of HPV DNA and of HPV E6/E7 mRNA (P &lt; .05). The estimate of HPV attributable proportion defined by expression of E6/E7 mRNA was 0 and of p16INK4a was 7.3%.

Conclusions
The data in this systematic review is robust enough to contradict the possible participation of HPV in lung cancer carcinogenesis. Prophylactic vaccines targeting HPV cannot have the potential to prevent lung cancer.
Composition of soil bacterial communities associated with urban stormwater detention basins and their predicted functional roles in N cycle
Authors: Moghadam Sina V , Jafarzadeh Arash , Vadde Kiran Kumar , Matta Akanksha , Dessouky Samer , Hutchinson Jeffrey , Kapoor Vikram 
Published: July 2023

Abstract

Aims
Stormwater detention basins serve as vital components in mitigating the adverse effects of urban runoff, and investigating the microbial dynamics within these systems is crucial for enhancing their performance and pollutant removal capabilities. The aim of this study was to examine and compare the soil bacterial communities in two stormwater detention basins located on the Edwards Aquifer in Bexar County, Texas, USA, and evaluate how soil physiochemical properties may affect them.

Methods and Results
Each basin soil was sampled in two different seasons at varying depths and the structure of microbial communities was examined using paired end Illumina sequencing using V3 and V4 region of 16S rRNA gene. PICRUSt2 was used to predict functional genes in the nitrogen cycle. In addition, soil physicochemical properties such as pH, carbon, nitrogen, and phosphorus and particle size were examined. A beta diversity analysis revealed that basins had distinctive microbial communities. Additionally, soil particle size, phosphorus and ammonia significantly correlated with some of the dominant phyla in the basins. Proteobacteria and Acidobacteria showed a positive correlation with the relative abundances of nitrogen-cycling genes, while Actinobacteria showed a negative correlation.

Conclusions
This study evaluated the associations between soil physicochemical properties and microbial community dynamics in stormwater basins. The study also predicts the relative abundance of nitrogen cycling genes, suggesting shared functional traits within microbial communities. The findings have implications for understanding the potential role of microbial communities in nitrogen cycling processes and contribute to developing sustainable stormwater management strategies and protecting water quality in urban areas.
Evolutionary implications from lipids in membrane bilayers and photosynthetic complexes in cyanobacteria and chloroplasts
Authors: Kobayashi Koichi , Yoshihara Akiko , Kubota-Kawai Hisako 
Published: July 2023

Abstract
In biomembranes, lipids form bilayer structures that serve as the fluid matrix for membrane proteins and other hydrophobic compounds. Additionally, lipid molecules associate with membrane proteins and impact their structures and functions. In both cyanobacteria and the chloroplasts of plants and algae, the lipid bilayer of the thylakoid membrane consists of four distinct glycerolipid classes: monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sulfoquinovosyldiacylglycerol, and phosphatidylglycerol. These lipids are also integral components of photosynthetic complexes such as photosystem II and photosystem I. The lipid-binding sites within the photosystems, as well as the lipid composition in the thylakoid membrane, are highly conserved between cyanobacteria and photosynthetic eukaryotes, and each lipid class has specific roles in oxygenic photosynthesis. This review aims to shed light on the potential evolutionary implications of lipid utilization in membrane lipid bilayers and photosynthetic complexes in oxygenic photosynthetic organisms.
Selection of aptamers using β-1,3-glucan recognition protein-tagged proteins and curdlan beads
Authors: Kumagai Kazuyuki , Okubo Hiroki , Amano Ryo , Kozu Tomoko , Ochiai Masanori , Horiuchi Masataka , Sakamoto Taiichi 
Published: July 2023

Abstract
RNA aptamersare nucleic acids that are obtained using the systematic evolution of ligands by exponential enrichment (SELEX) method. When using conventional selection methods to immobilize target proteins on matrix beads using protein tags, sequences are obtained that bind not only to the target proteins but also to the protein tags and matrix beads. In this study, we performed SELEX using β-1,3-glucan recognition protein (GRP)-tags and curdlan beads to immobilize the acute myeloid leukaemia 1 (AML1) Runt domain (RD) and analysed the enrichment of aptamers using high-throughput sequencing. Comparison of aptamer enrichment using the GRP-tag and His-tag suggested that aptamers were enriched using the GRP-tag as well as using the His-tag. Furthermore, surface plasmon resonance analysis revealed that the aptamer did not bind to the GRP-tag and that the conjugation of the GRP-tag to RD weakened the interaction between the aptamer and RD. The GRP-tag could have acted as a competitor to reduce weakly bound RNAs. Therefore, the affinity system of the GRP-tagged proteins and curdlan beads is suitable for obtaining specific aptamers using SELEX.