bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reverse engineering for reconstructing baseline features of dry age-related macular degeneration in optical coherence tomography
Authors: Wang Shuxian , Wang Ziyuan , Vejalla Srimanasa , Ganegoda Anushika , Nittala Muneeswar Gupta , Sadda SriniVas Reddy , Hu Zhihong Jewel 
Published: December 2022

AbstractAge-related macular degeneration (AMD) is the most widespread cause of blindness and the identification of baseline AMD features or biomarkers is critical for early intervention. Optical coherence tomography (OCT) imaging produces a 3D volume consisting of cross sections of retinal tissue while fundus fluorescence (FAF) imaging produces a 2D mapping of retina. FAF has been a good standard for assessing dry AMD late-stage geographic atrophy (GA) while OCT has been used for assessing early AMD biomarkers beyond as well. However, previous approaches in large extent defined AMD features subjectively based on clinicians’ observation. Deep learning—an objective artificial intelligence approach, may enable to discover ’true’ salient AMD features. We develop a novel reverse engineering approach which bases on the backbone of a fully convolutional neural network to objectively identify and visualize AMD early biomarkers in OCT from baseline exams before significant atrophy occurs. Utilizing manually annotated GA regions on FAF from a follow-up visit as ground truth, we segment GA regions and reconstruct early AMD features in baseline OCT volumes. In this preliminary exploration, compared with ground truth, we achieve baseline GA segmentation accuracy of 0.95 and overlapping ratio of 0.65. The reconstructions consistently highlight that large druse and druse clusters with or without mixed hyper-reflective focus lesion on baseline OCT cause the conversion of GA after 12 months. However, hyper-reflective focus lesions and subretinal drusenoid deposit lesions alone are not seen such conversion after 12 months. Further research with larger dataset would be needed to verify these findings.
A Drosophila model of the neurological symptoms in Mpv17-related diseases
Authors: Kodani Atsushi , Yamaguchi Mizuki , Itoh Ririka , Huynh Man Anh , Yoshida Hideki 
Published: December 2022

AbstractMutations in the Mpv17 gene are responsible for MPV17-related hepatocerebral mitochondrial DNA depletion syndrome and Charcot–Marie–Tooth (CMT) disease. Although several models including mouse, zebrafish, and cultured human cells, have been developed, the models do not show any neurological defects, which are often observed in patients. Therefore, we knocked down CG11077 (Drosophila Mpv17; dMpv17), an ortholog of human MPV17, in the nervous system in Drosophila melanogaster and investigated the behavioral and cellular phenotypes. The resulting dMpv17 knockdown larvae showed impaired locomotor activity and learning ability consistent with mitochondrial defects suggested by the reductions in mitochondrial DNA and ATP production and the increases in the levels of lactate and reactive oxygen species. Furthermore, an abnormal morphology of the neuromuscular junction, at the presynaptic terminal, was observed in dMpv17 knockdown larvae. These results reproduce well the symptoms of human diseases and partially reproduce the phenotypes of Mpv17-deficient model organisms. Therefore, we suggest that neuron-specific dMpv17 knockdown in Drosophila is a useful model for investigation of MPV17-related hepatocerebral mitochondrial DNA depletion syndrome and CMT caused by Mpv17 dysfunction.
Decarbonization scenarios and carbon reduction potential for China’s road transportation by 2060
Authors: Lu Quanying , Duan Hongbo , Shi Huiting , Peng Binbin , Liu Yi , Wu Tian , Du Huibin , Wang Shouyang 
Published: December 2022

AbstractThe transportation sector is a crucial source of greenhouse gas emissions, and the degree of its low-carbon transformation is closely related to the achievement of China’s carbon neutrality. Based on high-frequency passenger vehicle sales data and motor vehicle real-time monitoring big data, we developed a low-carbon transition planning model of China road transport (CRT-LCTP) to explore the pathways toward carbon neutrality. The study found that although the number of new energy vehicles (NEVs) increased four times from 2016 to 2019, the average annual growth rate of road traffic emissions was still as high as 20.5%. The current transportation electrification may only reduce 0.6% of the total emissions in this sector, and it could be increased to 1.4% if the electricity completely came from clean energy. Under the enhanced policy scenario, the transport sector could peak its carbon emissions at around of 2030, with the peak level being 1330.98 Mt. Transportation electrification along could not meet the climate targets in 2060, and the continued inertia of fuel vehicles will slow the path of the road transport toward carbon neutrality, which depends on the forced elimination of fuel vehicles and more substantive decarbonization measures.
The Standard Operating Procedures in COVID-19 Pandemic for Periodontal Aerosol-Generating Procedures: A Process Audit
Authors: Haseeb Muhammad , Khalid Naima , Syed Azeem Ul Yaqin , Khan Zubair Ahmed , Qureshi Farheen , Ahsen Iftikhar 
Published: December 2022

Abstract
Objective This study aims to audit the process of patient management with aerosol-generating procedure (ultrasonic scaling) while adherence to the guidelines for health care workers (HCWs) during the coronavirus disease 2019 (COVID-19).
Materials and Methods Audits records at the Department of Periodontology at University College of Medicine and Dentistry Hospital, Lahore, Pakistan were collected (prospectively) over the period of October 1 to November 30, 2020 (1st cycle) and December 14, 2020 to February 12, 2021 (2nd cycle). The audit was divided into three components based on the guidelines: (1) physical environment, (2) patients/appointments, and (3) COVID standard operating procedures related to HCWs.
Results The recommended physical layout and procedural factors, as suggested by the guidelines for dental clinics, were observed during the first cycle of audit, and discrepancy of ventilation system was fixed after the first cycle. Audit team reported the observance of fallow time three times daily, which revealed 83.3% observance of fallow time.Later in the second cycle when the extraoral high-volume air evacuator was installed, the fallow time was reduced to 15 minutes and not only five procedural slots per day were created but fallow time was also observed 100% of the time.
Conclusion Following the standard guidelines resulted in more efficient working environment and lesser risk for HCWs while performing aerosol-generating procedures.
Role of Multidetector Computed Tomography in Diagnosis of Acquired Gastrointestinal Fistulas
Authors: Arora Gitanjali , Badhe Padma V. 
Published: December 2022

Abstract
Introduction Fistulas are abnormal communication between two epithelialized surfaces. Gastrointestinal fistulas are communication between the gut and another epithelialized surface. Fistulas are classified according to anatomic (internal or external), physiologic (output volume), and etiologic characteristics. In the case of clinical suspicion of a fistula, a multidisciplinary approach helps in diagnosing and management. Multidetector computed tomography (MDCT) has an advantage over other imaging modalities due to its ability to reconstruct high-resolution images in seconds, which limits motion or peristalsis artifacts, and is ideal for patients who are uncooperative or who are seriously ill.
Aim Evaluation of MDCT as an initial tool in the diagnosis and characterization of gastrointestinal fistulas.
Methods During this prospective observational study, MDCT was used to assess patients with clinical suspicion of gastrointestinal fistulas. When necessary, contrast agents were used to identify the enteric fistulous tract. The etiology and characterization of the fistulas were determined. Further, the gastrointestinal fistulas were confirmed via endoscopy, cystoscopy, or surgery.
Results The most common type of gastrointestinal fistula is enterocutaneous fistula (ECF) (39%) and the most common cause of gastrointestinal fistulas is postoperative (47%). ECFs were classified according to their etiology, anatomy, and favorable characteristics (85% favorable) along with complexity (64% complex) to aid in the management process. In addition to pancreaticopleural fistulas (22%), biliary (11%), esophageal (8%), and pelvic fistulas (19%) were also observed. There were 19% of fistulas (esophageal and biliary) that were asymptomatic. Endoscopy confirmed such asymptomatic fistulas that were not convincingly detected on CT.
Conclusion In this study, we concluded that with the appropriate clinical history, MDCT can accurately depict enteric fistulas. In addition to characterizing fistulas, MDCT is equally useful for detecting secondary complications like inflammation, obstruction, or abscesses.
Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements by the new software CircFusion
Authors: Dal Molin Anna , Tretti Parenzan Caterina , Gaffo Enrico , Borin Cristina , Boldrin Elena , Meyer Lueder H , te Kronnie Geertruij , Bresolin Silvia , Bortoluzzi Stefania 
Published: December 2022

Abstract
Chromosomal translocations in cancer genomes, key players in many types of cancers, generate chimeric proteins that drive oncogenesis. Genomes with chromosomal rearrangements can also produce fusion circular RNAs (f-circRNAs) by backsplicing of chimeric transcripts, as first shown in leukemias with PML::RARα and KMT2A::MLLT3 translocations and later in solid cancers. F-circRNAs contribute to the oncogenic processes and reinforce the oncogenic activity of chimeric proteins. In leukemia with KMT2A::AFF1 (MLL::AF4) fusions, we previously reported specific alterations of circRNA expression, but nothing was known about f-circRNAs. Due to the presence of two chimeric sequences, fusion and backsplice junctions, the identification of f-circRNAs with available tools is challenging, possibly resulting in the underestimation of this RNA species, especially when the breakpoint is not known. We developed CircFusion, a new software tool to detect linear fusion transcripts and f-circRNAs from RNA-seq data, both in samples for which the breakpoints are known and when the information about the joined exons is missing. CircFusion can detect linear and circular chimeric transcripts deriving from the main and reciprocal translocations also in the presence of multiple breakpoints, which are common in malignant cells. Benchmarking tests on simulated and real datasets of cancer samples with previously experimentally determined f-circRNAs showed that CircFusion provides reliable predictions and outperforms available methods for f-circRNA detection. We discovered and validated novel f-circRNAs in acute leukemia harboring KMT2A::AFF1 rearrangements, leading the way to future functional studies aimed to unveil their role in this malignancy.
CoDe: a web-based tool for codon deoptimization
Authors: Sharma Divya , Baas Tracey , Nogales Aitor , Martinez-Sobrido Luis , Gromiha M Michael 
Published: December 2022

Abstract

Summary
We have developed a web-based tool, CoDe (Codon Deoptimization) that deoptimizes genetic sequences based on different codon usage bias, ultimately reducing expression of the corresponding protein. The tool could also deoptimize the sequence for a specific region and/or selected amino acid(s). Moreover, CoDe can highlight sites targeted by restriction enzymes in the wild-type and codon-deoptimized sequences. Importantly, our web-based tool has a user-friendly interface with flexible options to download results.

Availability and implementation
The web-based tool CoDe is freely available at https://web.iitm.ac.in/bioinfo2/codeop/landing_page.html.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Assessing renewable-energy potential and feasibility in Tehran’s buildings
Authors: Farahani Mehrab Hemmati , Namazzadeh Marjan , Farahani Azin Hemmati 
Published: December 2022

AbstractThis article examines the results of using renewable energy to reduce the energy consumption of buildings significantly. In particular, it looks at the results in a country such as Iran, which has a high potential for using solar energy. A comparison of the energy consumption of selected case samples based on the type of ownership of private, government and municipal buildings in 22 districts of Tehran has been analysed. Using data for energy consumption and Strengths, Weaknesses, Opportunities, Threats analysis includes open and usable spaces for installing renewable-energy systems in 10% of public buildings, 4% of private facilities and 10% of municipal buildings. The results of this study show that the average energy consumption of buildings in Tehran is almost four times the global average. Iran has ~300 days of sunlight for installing solar panels in any place where solar energy is in direct contact with the Sun. Thus, it allows the building to use the energy absorbed by the discussions in all seasons. In 2050, this country could play a decisive role in producing renewable energy. In addition, solar energy may reduce fossil-fuel consumption and production costs.
Empagliflozin: Validation of Stability-Indicating LC Method and in silico Toxicity Studies
Authors: da Silva Andressa Tassinari , Brabo Gabriela Rossi , Porto Douglas dos Santos , da Silva Jonco Jaizor , Bajerski Lisiane , Paula Fávero Reisdorfer , Paim Clésio Soldateli 
Published: December 2022

Abstract
A new stability-indicating liquid chromatography method was developed for the quantification of empagliflozin and two synthetic impurities. The chromatographic conditions included Spherisorb® RP-18 column (150 × 4.6 mm, 5 μm) with a PDA detector, using acetonitrile and formic acid (pH 4.0) as mobile phase in gradient elution and flow-rate of 1.2 mL·min−1. The gradient increasing from 51 to 100% acetonitrile until 11.00 min, followed by decreasing the solvent from 100% to the initial ratio from 11.01 to 15.00 min. The method was validated according to International Council of Harmonization guidelines. The LOD and LOQ values for impurities A and B were 35 and 15 ng·mL−1, respectively, (for LOD) and 115 and 35 ng.mL−1, respectively (for LOQ). The method was linear in the range of 80–140, 115–1150 and 35–350 ng·mL−1 for EMPA, impurities A and B, respectively, and the correlation coefficient were &gt; 0.999 in all situations, indicating the method good linearity. The developed method showed a good recovery for empagliflozin and added impurities. The method has proven to be precise, demonstrated values less than 2.0% to empagliflozin and 5.0% to synthetic impurities, robust and selective with no interference from other products in the determination of analytes. The in silico toxicity prediction suggested that the impurities do not present any toxicity risk for the parameters evaluated.
The Capitulations Syndrome: Why Revisionist Powers Leverage Post-Colonial Sensibilities toward Post-Imperial Projects
Authors: Fisher-Onar Nora 
Published: December 2022

AbstractThis article confronts a puzzle regarding revisionist powers: How to make sense of states whose behavior combines “post-colonial” critique of Western hegemony with “post-imperial” projects at home and in near abroads? Answers to this question are often informed by realist notions of great power competition that tend to read revisionist critique of the West as either epiphenomenal or due to intrinsic enmity.This piece proposes an alternative—the “capitulations syndrome”—which is developed via the Ottoman/Turkish experience and the literature on ontological insecurity. The syndrome combines “moral injury” at subordination to the West with attempts to elevate a state's status within Western-dominated international society. Anxieties produced by this paradox are managed via state narratives that celebrate select glories and traumas. This results in an exceptionalist sense of national “Self” that—when confronted—can lead to outrage at “Others” of the state story. The syndrome, I argue, both shapes broad imaginaries and is instrumentalized by policymakers. Thus, calls for global justice vis-à-vis Western hegemony can coexist with hegemonic projects nearer home.Identifying a series of family resemblances with China and Iran, I conclude by underscoring the article's main contributions: (1) its empirical study of the (post-)Ottoman experience as a case of revisionist former empires, (2) its analytical tool—the capitulations syndrome—with which to read comparative patterns, and (3) its epistemological corrective to international relations’ blindspot regarding actors with both “post-colonial” and “post-imperial” features. This hybrid condition enables revisionist former empires to invoke post-colonial solidarities in pursuit of post-imperial projects.
Can modified Dunn radiographs be an alternative to standing AP pelvis radiographs in the evaluation of pincer femoroacetabular impingement?
Authors: Cici Hakan , Zeybek Hakan , Hapa Onur 
Published: December 2022

ABSTRACT
The purpose of this study was to compare modified Dunn radiographs with standing anteroposterior (AP) pelvis radiographs in respect of the tilt ratio, lateral centre-edge angle (LCEA), crossover sign, crossover percentage and joint space width measurements. The study hypothesis was that modified Dunn radiographs could be an alternative method to standing AP pelvis images in the evaluation of pincer-type femoroacetabular impingement (FAI). The study included 31 patients with a mean age of 42 years (range: 29–55 years) who had modified Dunn and standing AP pelvis radiographs taken in the radiological evaluation of non-traumatic hip pain between July 2018 and September 2022. Similar tilt ratio values were obtained on standing AP and modified Dunn images (P = 0.986). Joint space width showed a decrease in the transition from the modified Dunn position to the standing position, but the difference was not statistically significant (P = 0.161). The mean LCEA was measured as 34° ± 4° in the standing position and as 35° ± 5° in the modified Dunn position. No statistically significant difference was determined in the number of patients with a crossover sign or the crossover percentage values in these patients (P &gt; 0.05). The data obtained in this study showed that there was no significant difference between images taken in the standing and modified Dunn positions in respect of radiological findings of pelvic tilt and pincer-type FAI. The modified Dunn radiograph is equivalent to the standing AP pelvis radiograph for the evaluation of pincer FAI.
Focal myositis in the foot: one unique case in the plantar aspect
Authors: Alkhatib Mohammad , Alneasan Moaaz , Aji Widad 
Published: December 2022

Abstract
We present a case of an acquired deformity of the toes of a young patient with no previous pathologic or traumatic history. Later, it emerged that it was ‘Focal Myositis’ at the Flexor Digitorum Brevis muscle of the right foot. The clinical course of the case involved a hard painless mass at the muscle belly that increased in size very slowly over several years, causing flexion contracture of the third toe without an accompanying skin lesion.
A novel presentation of alcohol-induced gastric necrosis: a case report
Authors: Silvers Jason , Dixit Shaili , Tan Khea , Masia Rachel , Pratt Abimbola , Bulauitan Constantine , Arumugam Dena , Kipnis Seth 
Published: December 2022

Abstract
Acute gastric necrosis is a rare condition with unknown pathogenesis. Existing literature describes acute esophageal necrosis as a result of excessive alcohol use; however, it is more difficult to find literature on alcohol-induced gastric necrosis. This condition may present with epigastric tenderness, vomiting or diarrhea with findings of pneumoperitoneum, gastric pneumatosis and portal venous gas on computed tomography. These patients can have complications such as septic shock, peritonitis and death. In this case report, we discuss a patient with a history of alcohol abuse who presented with acute gastric necrosis. On endoscopy, this patient was found to have a black necrotic gastric fundus and unusual erythematous changes to the mucosa. Prior research has identified other findings of patchy or diffuse circumferential black pigmentation of esophageal mucosa in patients with alcohol-induced esophageal necrosis, otherwise known as black esophagus. This case report aims to describe this novel presentation of alcohol-induced gastric necrosis.
Inadequate sampling of the soundscape leads to overoptimistic estimates of recogniser performance: a case study of two sympatric macaw species
Authors: Lewis Thomas C. , Vargas Ignacio Gutiérrez , Beckerman Andrew P , Childs Dylan Z. 
Published: December 2022

AbstractPassive acoustic monitoring (PAM) – the use of autonomous recording units to record ambient sound – offers the potential to dramatically increase the scale and robustness of species monitoring in rainforest ecosystems. PAM generates large volumes of data that require automated methods of target species detection. Species-specific recognisers, which often use supervised machine learning, can achieve this goal. However, they require a large training dataset of both target and non-target signals, which is time-consuming and challenging to create. Unfortunately, very little information about creating training datasets for supervised machine learning recognisers is available, especially for tropical ecosystems. Here we show an iterative approach to creating a training dataset that improved recogniser precision from 0.12 to 0.55. By sampling background noise using an initial small recogniser, we can address one of the significant challenges of training dataset creation in acoustically diverse environments. Our work demonstrates that recognisers will likely fail in real-world settings unless the training dataset size is large enough and sufficiently representative of the ambient soundscape. We outline a simple workflow that can provide users with an accessible way to create a species-specific PAM recogniser that addresses these issues for tropical rainforest environments. Our work provides important lessons for PAM practitioners wanting to develop species-specific recognisers for acoustically diverse ecosystems.
Novel lentiviral vectors for gene therapy of sickle cell disease combining gene addition and gene silencing strategies
Authors: Brusson Mégane , Chalumeau Anne , Martinucci Pierre , Romano Oriana , Poletti Valentina , Scaramuzza Samantha , Ramadier Sophie , Masson Cecile , Ferrari Giuliana , Mavilio Fulvio , Cavazzana Marina , Amendola Mario , Miccio Annarita 
Published: December 2022

AbstractSickle cell disease (SCD) is due to a mutation in the β-globin (HBB) gene causing the production of the toxic sickle hemoglobin (HbS, a2βS2). Transplantation of autologous hematopoietic stem/progenitor cells (HSPCs) transduced with lentiviral vectors (LVs) expressing an anti-sickling β-globin (βAS) is a promising treatment; however, it is only partially effective and patients still present elevated HbS levels. Here, we developed a bifunctional LV expressing βAS3-globin and an artificial microRNA (amiR) specifically downregulating βS-globin expression with the aim of reducing HbS levels and favoring βAS3 incorporation into Hb tetramers. Efficient transduction of SCD HSPC by the bifunctional LV led to a substantial decrease of βS-globin transcripts in HSPC-derived erythroid cells, a significant reduction of HbS+red cells and effective correction of the sickling phenotype, outperforming βAS gene addition andBCL11Agene silencing strategies. The bifunctional LV showed a standard integration profile and neither the HSPC viability, engraftment and multi-lineage differentiation nor the erythroid transcriptome and miRNAome were affected by the treatment, confirming the safety of this therapeutic strategy. In conclusion, the combination of gene addition and gene silencing strategies can improve the efficacy of current LV-based therapeutic approaches without increasing the mutagenic vector load, thus representing a novel treatment for SCD.