bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preferences of Tourists for the Comfort of the Semarang Old Town Area After Revitalization as a Heritage Tourism Destination in the City of Semarang
Authors: Puspitasari A Y , Rochani A , Khasanah Ramli W O S 
Published: April 2024

Abstract
Semarang Old Town Area has been designated as a National Cultural Heritage Area based on the Decree of the Minister of Education and Culture of the Republic of Indonesia Number 682/P/2020. Revitalization of the Semarang Old Town Area abbreviated as KKLS is carried out with the aim of sustainable development and providing the benefit of increasing economic value for the local community by making minor changes to historic buildings, as much as possible to maintain authenticity, and if changes are needed, they must be carried out with careful consideration. After the revitalization, KKLS became one of the popular destinations by offering views of old buildings along with their historical value, being able to have a good influence on increasing economic activity and being able to become a strong tourist attraction for tourists. However, there are still problems related to the provision of public facilities such as toilets, parking, and lighting. Convenience is basically not only related to the availability of facilities but also regarding the psychology felt by tourists towards these facilities. The purpose of this research is to find out the comfort level of post-revitalization KKLS based on tourist preferences. The results of this research show that tourist feel comfortable, this is proven by six of the eight variables stating that they area comfortable.
Heart Rate Acceleration and Deceleration Capacities Associated With 24-Hour Circadian Blood Pressure Variation of Hypertension Patients
Authors: Wang Jijing , Xu Jinyi , Zhang Hengyuan , Qiu Yanyan , Zhang Na , Yan Fei , Ji Yanfang 
Published: April 2024

Abstract

OBJECTIVE
To observe the relationship between 24-hour ambulatory blood pressure circadian rhythm and heart rate acceleration (AC), deceleration capacities (DC) in patients with hypertension.

METHODS
A total of 198 patients with essential hypertension were included and were monitored by 24-hour ambulatory blood pressure. Based on the nocturnal decline rate of systolic blood pressure, patients were divided into 2 groups: dippers (decline rate 10%–20%, n = 58) and non-dippers (decline rate &lt;10%, n = 140). DC and AC values were calculated based on dynamic electrocardiogram data and compared between 2 groups. Pearson correlation analysis was used to analyze the correlation between DC, AC, and blood pressure and circadian blood pressure variation. Multivariate logistic regression analysis was used to analyze the influencing factors of non-dippers.

RESULTS
Compared with dippers, AC increased, while DC, standard deviation of normal R–R intervals (SDNN), percentage of heart beats with difference between adjacent normal RR intervals &gt;50 ms in the total number of NN intervals (PNN50%) decreased in non-dippers (P &lt; 0.05). Pearson analysis showed that AC was positively correlated to nighttime systolic blood pressure (r = 0.297), slowest heart rate (r = 0.221) and negatively correlated to SDNN (r = −0.233) and PNN50 (r = −0.238), while DC was negatively correlated to nighttime systolic blood pressure (r = −0.300), 24-hour average heart rate (r = −0.144), slowest heart rate (r = −0.213), and positively correlated to SDNN (r = 0.230), PNN50 (r = 0.267) (all P &lt; 0.05). Multivariate logistic regression analysis showed that in the model included AC, AC (odds ratio [OR] = 1.320, 95% confidence interval [CI] 1.102–1.580, P = 0.003), age (OR = 1.029, 95% CI 1.001–1.057, P = 0.039), and 24-hour average heart rate (OR = 1.062, 95% CI 1.010–1.116, P = 0.02) were independent risk factors for non-dippers, while in the model included DC, DC (OR = 0.824, 95% CI 0.709–0.956, P = 0.011), age (OR = 1.027, 95% CI 1.001–1.055, P = 0.046), and 24-hour average heart rate (OR = 1.058, 95% CI 1.007–1.113, P = 0.025) were independent risk factors for non-dippers.

CONCLUSIONS
AC increases and DC decreases in patients with non-dipper hypertension. Nighttime systolic blood pressure positively correlates with AC and negatively correlates with DC. AC and DC are independent risk factors for abnormal circadian rhythm of blood pressure in hypertensives.
Synthesis and optical properties of tris(2,4,6-trichlorophenyl)methyl-type luminescent radicals bearing multiple carbazole substituents
Authors: Yang Peiyuan , Nagata Masakazu , Fukumoto Hiroki , Nakashima Kouichi , Yasuda Takuma , Agou Tomohiro 
Published: April 2024

Abstract
Two tris(2,4,6-trichlorophenyl)methyl (TTM)-type luminescent radicals, TTM-(3PCz)2 and TTM-(3PCz)3, bearing 2 and 3 9-phenylcarbazol-3-yl (3PCz) substituents, respectively, were synthesized and characterized. The photobleaching of these radicals was suppressed compared with that of previously reported TTM-type luminescent radicals, suggesting a favorable effect of the multiple electron-donating 3PCz groups on the photostability of the TTM-type radicals.
Re-examining Correlations Between Synonymous Codon Usage and Protein Bond Angles in Escherichia coli
Authors: Akeju Opetunde J , Cope Alexander L 
Published: April 2024

Abstract
Rosenberg AA, Marx A, Bronstein AM (Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. Nat Commun. 2022:13:2815) recently found a surprising correlation between synonymous codon usage and the dihedral bond angles of the resulting amino acid. However, their analysis did not account for the strongest known correlate of codon usage: gene expression. We re-examined the relationship between bond angles and codon usage by applying the approach of Rosenberg et al. to simulated protein-coding sequences that (i) have random codon usage, (ii) codon usage determined by mutation biases, and (iii) maintain the general relationship between codon usage and gene expression via the assumption of selection-mutation-drift equilibrium. We observed correlations between dihedral bond angle and codon usage when codon usage is entirely random, indicating possible conflation of noise with differences in bond angle distributions between synonymous codons. More relevant to the general analysis of codon usage patterns, we found surprisingly good agreement between the analysis of the real sequences and the analysis of sequences simulated assuming selection-mutation-drift equilibrium, with 91% of significant synonymous codon pairs detected in the former were also detected in the latter. We believe the correlation between codon usage and dihedral bond angles resulted from the variation in codon usage across genes due to the interplay between mutation bias, natural selection for translation efficiency, and gene expression, further underscoring these factors must be controlled for when looking for novel patterns related to codon usage.
In vitro and in vivo metabolic study of three new psychoactive β-keto-arylcyclohexylamines
Authors: Xu Linhao , Yan Hui , Tang Yiling , Liu Yu , Xiang Ping , Hang Taijun 
Published: April 2024

Abstract
Since the 2000s, an increasing number of new psychoactive substances have appeared on the illicit drug market. β-Keto-arylcyclohexylamine compounds play important pharmacological roles in anesthesia; however, because these new psychoactive substances have rapidly increasing illicit recreational use, the lack of detailed toxicity data are of particular concern. Therefore, analysis of their metabolites can help forensic personnel provide references and suggestions on whether a suspect has taken an illicit new psychoactive β-keto-arylcyclohexylamine. The present study investigated the in vitro and in vivo metabolism and metabolites of three β-keto-arylcyclohexylamines: deschloro-N-ethyl-ketamine, fluoro-N-ethyl-ketamine and bromoketamine. In vitro and in vivo models were established using zebrafish and human liver microsomes for analysis of Phase I and Phase II metabolites by liquid chromatography–high-resolution mass spectrometry. Altogether, 49 metabolites were identified. The results were applied for the subject urine samples of known fluoro-N-ethyl-ketamine consumer screen analysis in forensic cases. Hydroxy-deschloro-N-ethyl-ketamine, hydroxy-fluoro-N-ethyl-ketamine and hydroxy-bromoketamine were recommended as potential biomarkers for documenting intake in clinical and forensic cases.
PypKa server: online pKa predictions and biomolecular structure preparation with precomputed data from PDB and AlphaFold DB
Authors: Reis Pedro B P S , Clevert Djork-Arné , Machuqueiro Miguel 
Published: April 2024

Abstract
When preparing biomolecular structures for molecular dynamics simulations, pKa calculations are required to provide at least a representative protonation state at a given pH value. Neglecting this step and adopting the reference protonation states of the amino acid residues in water, often leads to wrong electrostatics and nonphysical simulations. Fortunately, several methods have been developed to prepare structures considering the protonation preference of residues in their specific environments (pKa values), and some are even available for online usage. In this work, we present the PypKa server, which allows users to run physics-based, as well as ML-accelerated methods suitable for larger systems, to obtain pKa values, isoelectric points, titration curves, and structures with representative pH-dependent protonation states compatible with commonly used force fields (AMBER, CHARMM, GROMOS). The user may upload a custom structure or submit an identifier code from PBD or UniProtKB. The results for over 200k structures taken from the Protein Data Bank and the AlphaFold DB have been precomputed, and their data can be retrieved without extra calculations. All this information can also be obtained from an application programming interface (API) facilitating its usage and integration into existing pipelines as well as other web services. The web server is available at pypka.org.
PPI3D: a web server for searching, analyzing and modeling protein–protein, protein–peptide and protein–nucleic acid interactions
Authors: Dapkūnas Justas , Timinskas Albertas , Olechnovič Kliment , Tomkuvienė Miglė , Venclovas Česlovas 
Published: April 2024

Abstract
Structure-resolved protein interactions with other proteins, peptides and nucleic acids are key for understanding molecular mechanisms. The PPI3D web server enables researchers to query preprocessed and clustered structural data, analyze the results and make homology-based inferences for protein interactions. PPI3D offers three interaction exploration modes: (i) all interactions for proteins homologous to the query, (ii) interactions between two proteins or their homologs and (iii) interactions within a specific PDB entry. The server allows interactive analysis of the identified interactions in both summarized and detailed manner. This includes protein annotations, structures, the interface residues and the corresponding contact surface areas. In addition, users can make inferences about residues at the interaction interface for the query protein(s) from the sequence alignments and homology models. The weekly updated PPI3D database includes all the interaction interfaces and binding sites from PDB, clustered based on both protein sequence and structural similarity, yielding non-redundant datasets without loss of alternative interaction modes. Consequently, the PPI3D users avoid being flooded with redundant information, a typical situation for intensely studied proteins. Furthermore, PPI3D provides a possibility to download user-defined sets of interaction interfaces and analyze them locally. The PPI3D web server is available at https://bioinformatics.lt/ppi3d.
A meta-analysis comparing treatment of benign prostatic hyperplasia with holmium laser enucleation and photoselective greenlight vaporization
Authors: Wang Zhichao , Tan Zicheng , Qiu Mengzhen , Zhang Longyang 
Published: April 2024

Abstract

Background
We compared the safety and efficacy of treating benign prostatic hyperplasia with photoselective greenlight vaporization (PVP) versus holmium laser enucleation of the prostate (HoLEP).

Methods
Databases (PubMed, Embase, Cochrane Library, Chinese CBM, and CNKI) were searched for eligible studies evaluating HoLEP or PVP outcomes, published until May 2022. We analyzed the incidence of relative complications and postoperative outcomes, including the international prostate symptom score, maximum flow rate (Qmax), postvoid residual urine volume, quality of life index, and prostate-specific antigen levels.

Results
Eleven studies involving 4763 patients were included in this meta-analysis. The significant differences in postoperative Qmax at 1 month (mean difference [MD], 3.31, 95% confidence interval [CI], 0.45–6.16, p = 0.02, I
2, 92%), 3 months (MD, 2.78, 95% CI, 0.53–5.02, p = 0.02, I
2, 89%), 6 months (MD, 2.13, 95% CI, 1.11–3.15, p < 0.0001, I
2, 87%), and 12 months (MD, 3.98, 95% CI, 2.06–5.89, p < 0.0001, I
2, 58%) further confirmed unique advantage of HoLEP over PVP. We used forest plots to determine significant differences in the severe complication rates among patients in the PVP and HoLEP groups (odds ratio, 0.05, 95% CI, 0.01 to 0.28, p = 0.0005).

Conclusions
Holmium laser enucleation of the prostate and PVP showed comparable international prostate symptom scores, quality of life index, postvoid residual urine volumes, prostate-specific antigen levels, perioperative factors, and total complication rates. Compared with PVP, HoLEP had a greater Qmax 1 year postoperatively, decreased energy expenditure, and fewer high-grade complications. These results need to be verified in long-term follow-up studies with well-structured randomized controlled trials.
Lymphatic Mapping for LVA with Noncontrast Lymphatic Ultrasound: How We Do It
Authors: Hara Hisako , Ichinose Michiru , Shimomura Fumika , Kawahara Mari , Mihara Makoto 
Published: April 2024

Summary:
Recently, lymphatic ultrasonography has received increasing attention. Although there are several reports on contrast-enhanced lymphatic ultrasound as a preoperative examination for lymphaticovenous anastomosis (LVA), we have been reporting the usefulness of preoperative noncontrast lymphatic ultrasound. In this article, the detailed procedure for conducting lymphatic ultrasound during the preoperative examination of LVA is thoroughly described. The only items required for lymphatic ultrasound are an ultrasound device, an echo jelly, a straw for marking, and a marker. We use an ordinary ultrasound device with an 18-MHz linear probe. We apply the Doppler, Crossing, Uncollapsible, Parallel, and Superficial fascia index to identify the lymphatic vessels. While imagining the course of the lymph vessels, we position the probe perpendicular to the long axis of the lymphatic vessels. When a vessel is found under the superficial fascia, the probe is moved proximally to trace the vessel’s path. If the vessel transverses a nearby vein without connecting to it, it is most likely a lymphatic vessel. To confirm, we ensure that the vessel does not exhibit coloration in the Doppler mode. As LVA is most effective when the dilated lymph vessels are anastomosed, we use lymphatic ultrasound to identify the most dilated lymphatic vessels in each lymphosome, and mark incision lines where suitable veins are in close proximity. No contrast agent is required; therefore, medical staff such as nurses and ultrasound technicians can autonomously conduct the test.
Management of Superficial and Deep Peroneal Nerve Neuromas with Targeted Muscle Reinnervation in Nonamputees: Operative Technique and Early Outcomes
Authors: Moradian Simon , Taritsa Iulianna C. , Sharma Sripadh , Mioton Lauren , Dumanian Gregory A. , Ko Jason H. 
Published: April 2024

Background:
Targeted muscle reinnervation (TMR), a surgical technique developed by the senior authors that coapts proximal ends of nerves to distal motor nerves of adjacent muscles, has demonstrated efficacy in the treatment and prevention of neuroma pain. The objective of this study is to describe the surgical technique for TMR of the superficial peroneal nerve (SPN) and deep peroneal nerve (DPN) in nonamputee patients and provide data on postoperative functional outcomes.

Methods:
A single-institution retrospective chart review was performed between March 2018 and April 2021. Patients were de-identified and included if they were nonamputees receiving TMR for pain in the peroneal nerve distribution. Data extracted included demographic information, symptoms before operation, relevant nerve coaptation, peri-, and postoperative complications, and long-term functional outcomes.

Results:
Of the 19 patients reviewed, 11 patients underwent TMR of the SPN alone: eight had complete resolution of their symptoms; two indicated partial improvement in pain; and one patient had no improvement. Four patients underwent TMR of the DPN alone: two patients had complete resolution of their pain, and two patients had partial improvement with pain. Four patients underwent TMR of both the SPN/DPN: two patients had complete resolution of their symptoms, and two patients were noted to have significant improvement but had persistent pain from prior foot operations. Average follow-up time was 260 days.

Conclusions:
TMR is a successful technique in the management of SPN and DPN neuroma pain. Our technique revealed excellent clinical outcomes, no procedure-specific complications, and improved subjective pain reports.
mARC1 in MASLD: Modulation of lipid accumulation in human hepatocytes and adipocytes
Authors: Jones Amanda K. , Bajrami Besnik , Campbell Morgan K. , Erzurumluoglu Abdullah Mesut , Guo Qiusha , Chen Hongxing , Zhang Xiaomei , Zeveleva Svetlana , Kvaskoff David , Brunner Andreas-David , Muller Stefanie , Gathey Vasudha , Dave Rajvee M. , Tanner James W. , Rixen Sophia , Struwe Michel A. , Phoenix Kathryn , Klumph Kaitlyn J. , Robinson Heather , Veyel Daniel , Muller Annkatrin , Noyvert Boris , Bartholdy Boris Alexander , Steixner-Kumar Agnes A. , Stutzki Jan , Drichel Dmitriy , Omland Steffen , Sheehan Ryan , Hill Jon , Bretschneider Tom , Gottschling Dirk , Scheidig Axel J. , Clement Bernd , Giera Martin , Ding Zhihao , Broadwater John , Warren Curtis R. 
Published: April 2024

Background:
Mutations in the gene MTARC1 (mitochondrial amidoxime–reducing component 1) protect carriers from metabolic dysfunction–associated steatohepatitis (MASH) and cirrhosis. MTARC1 encodes the mARC1 enzyme, which is localized to the mitochondria and has no known MASH-relevant molecular function. Our studies aimed to expand on the published human genetic mARC1 data and to observe the molecular effects of mARC1 modulation in preclinical MASH models.

Methods and Results:
We identified a novel human structural variant deletion in MTARC1, which is associated with various biomarkers of liver health, including alanine aminotransferase levels. Phenome-wide Mendelian Randomization analyses additionally identified novel putatively causal associations between MTARC1 expression, and esophageal varices and cardiorespiratory traits. We observed that protective MTARC1 variants decreased protein accumulation in in vitro overexpression systems and used genetic tools to study mARC1 depletion in relevant human and mouse systems. Hepatocyte mARC1 knockdown in murine MASH models reduced body weight, liver steatosis, oxidative stress, cell death, and fibrogenesis markers. mARC1 siRNA treatment and overexpression modulated lipid accumulation and cell death consistently in primary human hepatocytes, hepatocyte cell lines, and primary human adipocytes. mARC1 depletion affected the accumulation of distinct lipid species and the expression of inflammatory and mitochondrial pathway genes/proteins in both in vitro and in vivo models.

Conclusions:
Depleting hepatocyte mARC1 improved metabolic dysfunction–associated steatotic liver disease–related outcomes. Given the functional role of mARC1 in human adipocyte lipid accumulation, systemic targeting of mARC1 should be considered when designing mARC1 therapies. Our data point to plasma lipid biomarkers predictive of mARC1 abundance, such as Ceramide 22:1. We propose future areas of study to describe the precise molecular function of mARC1, including lipid trafficking and subcellular location within or around the mitochondria and endoplasmic reticulum.
Hepatitis delta testing trends in a US national cohort: An analysis of patient and provider-level predictive factors
Authors: John Binu V. , Amoli Mahmoud Manouchehri , Evon Donna M. , Wong Robert , Dahman Bassam 
Published: April 2024

Background:
The low prevalence of HDV infection in the United States could be attributed to insufficient testing rate, which can result in an underestimation of the true burden of HDV. The primary objective of this study is to quantify the prevalence of and factors associated with HDV antibody (anti-HDV) or RNA testing, among participants with positive HBsAg in the Veterans Health Administration (VHA).

Methods:
We conducted a retrospective cohort study of participants who tested positive for HBsAg between January 2000 and December 2022 within the VHA. We identified those who were tested for HDV, and patient and provider-level factors associated with HDV testing.

Results:
Of 41,658 participants with positive HBsAg who had follow-up, 4438 (10.7%) were tested at least once for HDV, of which 135 (3.0%) were positive. Participants in the Northeast (adjusted odds ratio [aOR]: 1.30, 95% CI: 1.17–1.44, p<0.001), and receiving hepatology care (aOR: 1.38, 95% CI: 1.24–1.54, p<0.001) were more likely, while those in the Midwest (aOR: 0.69, 95% CI: 0.60–0.79, p<0.001), under the care of a primary care provider (aOR: 0.61, 95% CI: 0.50–0.74, p<0.001), Blacks (aOR: 0.85, 95% CI: 0.77–0.94, p=0.001), participants who were HCV antibody–positive (aOR: 0.89, 95% CI: 0.81–0.99, p=0.03), and participants who were HIV-positive (aOR: 0.80, 95% CI: 0.71–0.90, p<0.001) were less likely to be tested for HDV.

Conclusions:
HDV screening rates in the VHA remain low overall. Participants who are Black, living in the Midwest, patients who are HIV-positive, and patients who are HCV-positive are less likely to be tested for HDV. These results suggest that risk-based screening strategies are ineffective in the VHA and highlight the need for refining testing strategies to increase HDV screening rates.