bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequence and probiotic characterization of Lactobacillus delbrueckii subsp. indicus DC-3 isolated from traditional indigenous fermented milk
Authors: Chaudhari Deepti N. , Ahire Jayesh J. , Devkatte Anupama N. , Kulthe Amit S. 
Published: June 2024

Abstract

In this study, Lactobacillus delbrueckii subsp. indicus DC-3 was isolated from Indian traditional indigenous fermented milk Dahi and identified using whole genome sequencing. The safety of the strain was evaluated using both genetic and phenotypic analyses, such as the presence of virulence factors, mobile and insertion elements, plasmids, antibiotic resistance, etc. Besides this, the strain was comprehensively investigated for in vitro probiotic traits, biofilm formation, antibacterials, and exopolysaccharide (EPS) production. In results, the strain showed a single circular chromosome (3,145,837 bp) with a GC content of 56.73%, a higher number of accessory and unique genes, an open pan-genome, and the absence of mobile and insertion elements, plasmids, virulence, and transmissible antibiotic resistance genes. The strain was capable of surviving in gastric juice (83% viability at 3 h) and intestinal juice (71% viability at 6 h) and showed 42.5% autoaggregation, adhesion to mucin, 8.7% adhesion to xylene, and 8.3% adhesion to Caco-2 cells. The γ-hemolytic nature, usual antibiotic susceptibility profile, and negative results for mucin and gelatin degradation ensure the safety of the strain. The strain produced 10.5 g/L of D-lactic acid and hydrogen peroxide, capable of inhibiting and co-aggregating Escherichia coli MTCC 1687, Proteus mirabilis MTCC 425, and Candida albicans ATCC 14053. In addition, the strain showed 90 mg/L EPS (48 h) and biofilm formation. In conclusion, this study demonstrates that L. delbrueckii subsp. indicus DC-3 is unique and different than previously reported L. delbrueckii subsp. indicus strains and is a safe potential probiotic candidate.
Deep Learning-based Multi-class Object Tracking With Occlusion Handling Mechanism in Uav Videos
Authors: Micheal A Ancy , Micheal A Annie , Gopinathan Anurekha , Barathi B U Anu 
Published: June 2024

Abstract

Unmanned Aerial Vehicles (UAVs) play a crucial role in tracking-based applications, particularly in real-time situations such as rescue missions and surveillance. However, tracking objects with occlusion can be challenging, as it involves reidentifying objects with consistent identities. To address this issue, a novel multi-class object tracking methodology with occlusion handling has been proposed. This methodology employs You Only Look Once Neural Architecture Search (YOLO-NAS) and confluence-based object detection. YOLO-NAS has demonstrated superior detection with quantization-aware blocks and selective quantization, which is utilized for object tracking. Additionally, a Densely Connected Bidirectional LSTM tracker has been developed to use the feature representation and object locations from the detector. Furthermore, the methodology incorporates occlusion handling object association to re-identify objects in scenarios with occlusion or out-of-view situations. To evaluate the proposed framework, comparisons have been made with state-of-the-art models using UAV123, UAVDT, and VisDrone datasets. A detailed ablation study has been performed with UAV123 dataset. The proposed framework is observed to outperform other models with MOTA of 94.53%, Recall of 97.8%, Precision of 97.19%, F-score of 97.49% and Rel.ID of 9.26%.
No evidence of Bartonella infections in host-seeking Ixodes scapularis and I. pacificus ticks in the United States
Authors: Bai Ying , McClung Kristin L. , Osikowicz Lynn M. , Maes Sarah , Eisen Rebecca J. 
Published: June 2024

Abstract

Background
Bartonella spp. infect a variety of vertebrates throughout the world with generally high prevalence. Several Bartonella spp. are known to cause diverse clinical manifestations in humans and have been recognized as emerging pathogens. These bacteria are mainly transmitted by blood sucking arthropods, such as fleas and lice. The role of ticks in the transmission of Bartonella sp. is unclear.
Methods
A recently developed quadruplex PCR amplicon next generation sequencing approach that targets Bartonella-specific fragments on gltA, ssrA, rpoB, and groEL was applied to test host-seeking Ixodes scapularis ticks (n = 1641; consisting of 886 nymphs and 755 adults) collected in 23 states of the eastern United States and Ixodes pacificus ticks (n = 966; all nymphs) collected in California in the western United States for the presence of Bartonella DNA. These species were selected because they are common human biters and serve as vectors of pathogens causing the greatest number of vector-borne diseases in the United States.
Results
No Bartonella DNA was detected in any of the ticks tested by any target.
Conclusions
Owing to the lack of Bartonella detection in a large number of host-seeking Ixodes sp. ticks tested across a broad geographic region, our results strongly suggest that I. scapularis and I. pacificus are unlikely to contribute more than minimally, if at all, to transmission of Bartonella spp..
Exacerbation of Schistosomiasis Japonica in Shroom2-knockout Mice
Authors: Liu Wanling , Xiu Lei , Li Tao , Jiang Ning , Wan Yanmin , Jia Liqiu , Cun Yi , Wang Xiaoling , Lin Siran , Xie Yuxiang , Zhang Wei , Qiu Chao , Li Jian , Hu Wei , Wu Jing , Zhang Wenhong 
Published: June 2024

Abstract

Background
Shroom2 is an actin-binding protein known for its involvement in cell motility regulation and actin cytoskeleton remodeling. Schistosome eggs trigger the formation of granulomas, organized immune aggregates surrounding the eggs. However, the specific roles of Shroom2 in granuloma formation and evolution have not been elucidated.
Methods
Shroom2 knockout (KO) mice were utilized to investigate the impact of Shroom2 on the formation of Schistosomiasis japonicum (S. japonicum) egg granulomas. This study aimed to analyze the effects of Shroom2 deficiency on the host response to S. japonicum infection.
Results
KO mice exhibited a significantly elevated mortality rate when infected with S. japonicum. Furthermore, extensive lung tissue necrosis was observed following the implantation of S. japonicum eggs. The lungs of Shroom2 knockout mice displayed hyperinflammation after S. japonicum egg implantation, and the percentage of major immune cell populations was reduced.
Conclusion
Given the aforementioned results, we inferred that Shroom2 deficiency compromises the host’s ability to effectively defend against parasitic infections. This study highlights the crucial role of Shroom2 in immune response regulation during S. japonicum infection and suggests that Shroom2 is a potential key player in granuloma formation and overall host defense mechanisms.
One-step litchi like bimetallic nanozyme-assisted indirect competitive immunoassay for the detection of acetamiprid in vegetables
Authors: Liu BeiBei , Zhai Rongqi , Zhang Jie , Liu Guangyang , Huang Xiaodong , Lv Jun , Chen Jing , Liu Junjiang , Jin Maojun , Wang Jing , Xu Donghui , Chen Ge 
Published: June 2024

Abstract

The conventional enzyme-linked immunosorbent assay is limited in its ability to satisfy the increasing demand for advanced immunoassay due to its reliance on natural enzymes, low sensitivity, and narrow detection range. The development of nanozyme-assisted immunoassay is a viable approach to overcome this constraint. Therefore, a one-step litchi like nanozyme-assisted indirect competitive immunoassay was designed for the detection of acetamiprid. In this assay, litchi-like Au@Pt nanozyme (inexpensive, simple preparation, stable, and adjustable catalytic activity) were directly conjugated with antibodies as signal probes without using peroxidase-conjugated affinipure goat antimouse IgG (IgG-HRP). Acetamiprid competed with haptens to bind the Au@Pt probes. Subsequently, Au@Pt nanozymes, which exhibit peroxidase-like activity, were added to catalyze the oxidation of colorless 3,3′,5,5′-tetramethylbenzidine (TMB) in the presence of H2O2. The linear range, sensitivity, relative standard deviations (RSDs) ranged and limit of detection (LOD) were 1.85 ~ 327.19 µg/L, 25.58 µg/L, 0.46 ~ 10.35% and 0.78 µg/L, respectively, satisfying the requirement of immunoassay detection. In conclusion, the method exhibited high sensitivity, reproducibility and wide linear range for the detection of acetamiprid, while eliminating the need for IgG and simplifying the experimental procedure. The proposed indirect competitive immunoassay has great value for onsite sensitive detection of acetamiprid in vegetables.
The role of Tyr34 in proton-coupled electron transfer of human manganese superoxide dismutase
Authors: Borgstahl Gloria , Azadmanesh Jahaun , Slobodnik Katelyn , Struble Lucas , Cone Erika , Dasgupta Medhanjali , Lutz William , Kumar Siddhartha , Natarajan Amarnath , Coates Leighton , Weiss Kevin , Myles Dean , Kroll Thomas 
Published: June 2024

Abstract

Human manganese superoxide dismutase (MnSOD) plays a crucial role in controlling levels of reactive oxygen species (ROS) by converting superoxide (O2●−) to molecular oxygen (O2) and hydrogen peroxide (H2O2) with proton-coupled electron transfers (PCETs). The reactivity of human MnSOD is determined by the state of a key catalytic residue, Tyr34, that becomes post-translationally inactivated by nitration in various diseases associated with mitochondrial dysfunction. We previously reported that Tyr34 has an unusual pKa due to its proximity to the Mn metal and undergoes cyclic deprotonation and protonation events to promote the electron transfers of MnSOD. To shed light on the role of Tyr34 MnSOD catalysis, we performed neutron diffraction, X-ray spectroscopy, and quantum chemistry calculations of Tyr34Phe MnSOD in various enzymatic states. The data identifies the contributions of Tyr34 in MnSOD activity that support mitochondrial function and presents a thorough characterization of how a single tyrosine modulates PCET catalysis.
Catalyst and base-free, direct oxidation of chitin to lactic acid with hydrogen peroxide
Authors: Du Xiao , Li Tengfei , Wang Lumei , Ren Dezhang , Huo Zhibao 
Published: June 2024

Abstract

In recent years, the research on the conversion of chitin to high value-added chemicals has attracted more and more attention. At present, the method of preparing lactic acid from chitin mostly uses strong base or catalyst. These reaction systems have disadvantages such as corrosion of containers and harm to human body. Herein, a simple and effective method to convert chitin to organic acids in catalyst and base-free conditions is developed. The use of H2O2 only can efficiently convert chitin to organic acids in the absence of bases and catalysts. Under the optimal conditions of 30 mg chitin, 2.1 mL water, 0.9 mL H2O2 at 230 oC for 1.5 h, the lactic acid yield of chitin can reach 58.2% and the total organic acid yield can reach 84.0%. This work provides an efficient method for the resource utilization of chitin biomass.
Observation of higher-order time-dislocation topological modes
Authors: Lee Ching Hua , Zhang Jia-hui , Mei Feng , Li Yi , Ma Jie , Xiao Liantuan , Jia Suotang 
Published: June 2024

Abstract

Topological dislocation modes resulting from the interplay between spatial dislocations and
momentum-space topology have recently attracted significant interest. Here, we theoretically and
experimentally demonstrate time-dislocation topological modes which are induced by the interplay
between temporal dislocations and Floquet-band topology. By utilizing an extra physical dimension to represent the frequency-space lattice, we implement a two-dimensional Floquet higher-order
topological phase and observe time-dislocation induced π-mode topological corner modes in a three-
dimensional circuit metamaterial. Intriguingly, the realized time-dislocation topological modes exhibit spatial localization at the temporal dislocation, despite homogeneous in-plane lattice couplings across it. Our study opens a new avenue to explore the topological phenomena enabled by the interplay between real-space, time-space and momentum-space topology.
An assessment of postoperative pain management in a Ghanaian Hospital
Authors: Antwi Sara Agyemang , Tandoh Augustine , Woode Prof. Eric 
Published: June 2024

Abstract

Objective: Pain is an inevitable byproduct of surgery. Successful perioperative pain management is an ethical goal, and health professionals are obligated to limit complications and speed up patient recovery. This study aimed to examine the extent of pain relief and the impact of pain on patients’ quality of life.
Methods: This study included 217 surgical patients who underwent a variety of surgeries. The Brief Pain Inventory-Long Form (BPI-LF) and Medical Short Form-36 (SF-36) were successfully administered to 183 patients at one week and one month after surgery, respectively. The data thus obtained were analysed using SPSS (version 25).
Results: Among the 183 patients surveyed, 80.2% (n=174) were females, and 19.8% (n=43) were males. The mean age was 34.21 years (SD ±10.989). The percentage of pain relief ranged from 50-100%, and the average percentage of pain relief after the one-week interval was 80.05 ± SD 11.266. The Cronbach’s alpha values obtained for the 11 BPI items (pain severity and functional interference) were significant. The pain management index-1 (PMI-1 using ‘pain at its worst’) showed a mean of -0.7814 ± 1.127, indicating pain management inadequacy during the first 48 hrs after surgery. The nature of the surgery may have an impact on the quality of life of the patient.
Conclusion: Pain may be undermanaged in the first 48 hrs after surgery; however, pain management after one week was adequate.
Benchmarking the performance and uncertainty of machine learning models in estimating scour depth at sluice outlets
Authors: Le Xuan-Hien , Thu Hien Le Thi , Ho Hung Viet , Lee Giha 
Published: June 2024

ABSTRACT
This study investigates the performance of six machine learning (ML) models – Random Forest (RF), Adaptive Boosting (ADA), CatBoost (CAT), Support Vector Machine (SVM), Lasso Regression (LAS), and Artificial Neural Network (ANN) – against traditional empirical formulas for estimating maximum scour depth after sluice gates. Our findings indicate that ML models generally outperform empirical formulas, with correlation coefficients (CORR) ranging from 0.882 to 0.944 for ML models compared with 0.835–0.847 for empirical methods. Notably, ANN exhibited the highest performance, followed closely by CAT, with a CORR of 0.936. RF, ADA, and SVM performed competitive metrics around 0.928. Variable importance assessments highlighted the dimensionless densimetric Froude number (Fd) as significantly influential, particularly in RF, CAT, and LAS models. Furthermore, SHAP value analysis provided insights into each predictor's impact on model outputs. Uncertainty assessment through Monte Carlo (MC) and Bootstrap (BS) methods, with 1,000 iterations, indicated ML's capability to produce reliable uncertainty maps. ANN leads in performance with higher mean values and lower standard deviations, followed by CAT. MC results trend towards optimistic predictions compared with BS, as reflected in median values and interquartile ranges. This analysis underscores the efficacy of ML models in providing precise and reliable scour depth predictions.
Priawan in Indonesia: A Study of Transmasculine Female-to-Male Individuals
Authors: Artaria Myrtati Dyah , Alaydrus Sayf Muhammad , Budianto Azzah Kania , Prasetyo Dwi , Kaur Charanjit , Henneberg Maciej 
Published: June 2024

Topics surrounding transmasculinity, especially in Indonesia, are still overlooked, degraded, and understudied. This paper aims to explore the experience of priawan in Indonesia. Differentiating from the globally-renowned term ‘trans men’, a priawan identifies as a female-to-male transmasculine individual. We conducted in-depth interviews with eleven qualified informants. These interviews shed light on gender dysphoria or fluidity, gender-affirming processes, and discriminations they have faced, with hopes of proving and validating their existence. Eight of the informants express themselves as masculine and identify as lesbians. The most common gender-affirming process that they chose is name updating, followed by chest binding and hormone therapy. Five out of eleven reported having faced discrimination in various forms, such as verbal abuse, misgendering, stereotyping, and physical abuse. This study adds a new perspective on regional variability in transmasculine identities. Further research on chosen family dynamics and generational differences are encouraged to accentuate the visibility of transgender individuals in existing queer studies.
Learning Clinical Ethics for Medical Students in Clinical Phase
Authors: Ismail Taufik Suryadi , Assyifa Shofiya , Rusnaidi Rusnaidi 
Published: June 2024

Background: Clinical ethics is a method of clinical decision making ethically. The implementation of clinical ethics learning to clinical rotation students is one way to help students learn to make decisions about ethical dilemmas according to the learning outcomes in clinical rotations. There is no evaluation of the implementation of clinical ethics in clinical rotation learning in our institution, so a study is needed.Methods: This research is a descriptive study with a cross-sectional design using primary data through filling out online questionnaires (g-form) adopted from four box quadrant of clinical ethics by Johnsen, Siegler and Winslade. The respondent was clinical rotation students who underwent inpatient treatment from 10 clinical rotation stages at Zainoel Abidin Hospital. This research has been done from November until December 2022 by using consecutive sampling techniques with 75 respondent as minimum sampling. Results: A total of 87 respondents were involved in this study. This study shows that clinical ethics has been implemented in clinical rotation at Zainoel Abidin Hospital Banda Aceh. The most frequent implementation of clinical ethics is Obstetrics and Gynecology, and the least common is the Psychiatric. The implementation of clinical ethics learning in clinical rotation is already good, as seen from the majority of respondents who often get learning related to the medical indications quadrant (52.9%-58.6%), patient preference quadrant (44.8%-64.4%), the quality of life quadrant (57.5%-63.2%), and the contextual features quadrant (40.2%-59.8%).Conclusion: The implementation of clinical ethics learning in clinical rotation at Zainoel Abidin Hospital Banda Aceh is already good, although not optimal. Continuous learning of clinical ethics is necessary so that clinical rotation students are accustomed to solving ethical dilemmas in clinical situations.
The Noteworthiness of Constructive Feedback and Student-Reflection to Approach Competence-Based Curriculum: An Explanatory Study of Medical Schools in Indonesia
Authors: Salamy Achmad Yarziq Mubarak Salis , Claramita Mora , Suhoyo Yoyo 
Published: June 2024

Background: Competence-based medical curriculum requires the acquisition of complex abilities that should be assessed longitudinally. The programmatic assessment model can facilitate a complete picture of students' competencies. The five components of learning, assessment, supporting activities; and intermediate to final evaluation provide holistic learning experiences for students and mentors to participate in the learning strategies. We aim to assess the application of longitudinal components of the programmatic assessment model to the current assessment system based on student perceptions.Methods: This study used a cross-sectional mixed-method sequential explanatory design at six medical schools in Surabaya, East Java of Indonesia. The instrument was 43 items of validated questionnaire based on the five components and the focus group discussions. Results: This study obtained 442 respondents. The results reflected high reliability with a Cronbach alpha value of 0.969, and the validity test showed R arithmetic > R table (R table 0.128 for n 442). The current assessment system was perceived as ‘good’, with 3.9 on 5 points Likert scale; but the ‘supporting activities’ where reflection and feedback lied; was at the lowest score although insignificant. Students underlined the lack of formative aspects (reflection, feedback, mentorship, and middle evaluation).Conclusion: The overall assessment system is well-perceived by the students; however, the 'supportive activities' component has been minimally applied. So the 'assessment of previous learning' is still prominent in the current assessment system.
Description of The Professional Identity of First-Level Clinical Medical Students and The Various Factors That Facilitate Its Formation
Authors: Haryanti Nathalia , Puspadewi Natalia , Juliawati Veronica Dwi Jani , Anastasia Gisella 
Published: June 2024

Background: Identity formation is a longitudinal and continuous process. This study aimed to define: 1) the characteristics of professional identity (PI) of five first-year clinical students; 2) the role of clinical teachers and other factors that influenced PI formation during clinical rotations, and 3) how the learning process at the clinical level facilitates students to participate and gain recognition.Method: This was a qualitative phenomenological study. This study was open to any first-year clinical students who were undergoing their major clinical at the time of data collection and met the inclusion criteria. Indepth interview was conducted as soon as an interested student contacted the research team. At the end, five first-year clinical students were included in this study. All interviews were voice recorded and transcribed verbatim. Data was analyzed using thematic analysis.Results: a) Technical skills and internal values are two main components that formed their professional identities; b) Clinical teachers act as students’ role model and provide participants with the necessary recognition and opportunities to participate in a community of practice, which subsequently supported their PI formation during clinical rotation; c) participants’ PI formation was supported by various learning experiences embedded in their medical school’s curriculum. Conclusion: Technical skills and internal values are two professional identity components that defined a professional physician. Curriculum design as well as clinical teachers who closely interact with clinical students during their clinical rotations are two essential factors in creating a conducive learning environment that supports participants’ PI formation.