bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective study of antidepressant treatment of psychiatric patients with depressive disorders: treatment adequacy and outcomes
Authors: von Knorring Johanna , Baryshnikov Ilya , Jylhä Pekka , Talaslahti Tiina , Heikkinen Martti , Isometsä Erkki 
Published: November 2023

Abstract
Background
Despite numerous national depression care guidelines (DCGs), suboptimal antidepressant treatment may occur. We examined DCG concordance and depression treatment outcomes in psychiatric settings.

Methods
We evaluated treatment received and outcomes of 128 psychiatric out- and inpatients participating in the PEGAD (Pharmacoepidemiology and Pharmacogenetics of Antidepressant Treatment for Depressive Disorders) study at baseline, two weeks, and eight weeks using interviews and questionnaires. Inclusion criteria were ICD-10 diagnosis of a depressive disorder, a Patient Health Questionnaire-9 symptom (PHQ-9) score ≥ 10, and a new antidepressant prescribed. The primary outcome of the study was within-individual change in PHQ-9 scores.

Results
At baseline, patients had predominately recurrent (83%) and in 19% treatment-resistant depression (TRD). The median preceding duration of the current episode was 6.5 months. At eight weeks, 85% of the patients (n = 107) used a DCG-concordant antidepressant dose. However, due to the scarcity of antidepressant combinations and augmentations, fewer TRD than non-TRD patients (25% vs. 84%, p < 0.005) received adequate antidepressant treatment. Additionally, one-third of the patients received inadequate follow-up. Overall, only 53% received treatment compatible with DCG recommendations for adequate pharmacotherapy and follow-up. The mean decline in PHQ-9 scores (-3.8 ± SD 5.7) was significant (p < 0.0005). Nearly 40% of the patients reached a subthreshold level of depression (PHQ-9 < 10), predicted by a lower baseline PHQ-9 score, recurrent depression, and female sex. However, 45% experienced no significant clinical improvement (PHQ-9 score reduction < 20%).

Conclusions
Our findings suggest that inadequate treatment continues to occur in psychiatric care settings, particularly for TRD patients.
Muscle dynamics analysis by clustered categories during jogging in patients with anterior cruciate ligament deficiency
Authors: Li Haoran , Huang Hongshi , Zhang Si , Ren Shuang , Rong Qiguo 
Published: November 2023

Abstract
Background
Patients with anterior cruciate ligament (ACL) deficiency (ACLD) tend to have altered lower extremity dynamics. Little is known about the changes in dynamic function and activation during jogging in patients with ACLD.

Methods
Twenty patients with an injured ACL before ACL reconstruction (ACLD group) and nine healthy male volunteers (control group) were recruited. Each volunteer repeated the jogging experiment five times. Based on the experimental data measured, a musculoskeletal multibody dynamics model was employed to simulate the tibiofemoral joint dynamics during jogging. Eighteen muscles were used for analysis. The obtained dynamics data were used for clustering and curve difference analysis.

Results
The 18 muscles studied were divided into 3 categories. All the quadriceps, the soleus, the gastrocnemius, and the popliteus were classified as label 1. All the hamstrings were classified as label 2, and the sartorius muscles were classified as label 3. Among them, the classification of the short head of the biceps femoris was significantly different between the two groups (P < 0.001). The force curves of all 18 muscles and the between-group differences were studied according to clustered categories. Most muscle force in label 1 was approaching zero in the terminal stance phase, which was significantly lower than that in the control group (P < 0.05). The muscle force in label 2 had areas with significant differences in the stance phase. Muscle force in label 3 was significantly lower than that in the control group in the pre-swing phase.

Conclusions
This study showed that there are various changes of muscle function and activation in patients with ACLD. Through clustering and curve analysis, the joint reactions and changes of different muscle forces in the gait cycle between the ACLD and control groups could be further clarified.
A comparative study of flexible ureteroscopic lithotripsy for upper urinary tract stones in patients with prior urosepsis following emergency drainage via retrograde ureteral stent or percutaneous nephrostomy
Authors: Liao Sucai , Xu Xiang , Yuan Yuan , Tang Keiyui , Wei Genggeng , Lu Zhengquan , Xiong Lin 
Published: November 2023

Abstract
Background
Patients with urosepsis associated with upper urinary tract stones require further stone management after emergency drainage.

Objective
To evaluate the safety and efficacy of elective flexible ureteroscopic lithotripsy (F-URSL) for upper urinary tract stones in patients with prior urosepsis who have undergone emergency drainage using retrograde ureteral stent(RUS) or percutaneous nephrostomy (PCN).

Method
Between January 2017 and December 2021, clinical data were collected for 102 patients who underwent elective F-URSL following emergency drainage for urosepsis caused by upper ureteral or renal stones. The patients were categorized into two groups based on the drainage method used: the RUS group and the PCN group. The collected data included patient demographics, stone parameters, infection recovery after emergency drainage, and clinical outcomes post F-URSL. Subsequently, the data underwent statistical analysis.

Results
A total of 102 patients were included in the statistical analysis, with 58 (56.86%) in the RUS group and 44 (43.14%) in the PCN group. Among the patients, 84 (82.35%) were female and 18 (17.65%) were male, with an average age of 59.36 years. Positive urine cultures were observed in 71 (69.61%) patients. Successful drainage was achieved in all patients in both groups, and there were no significant differences in the time required for normalization of white blood cell count (WBC) and body temperature following drainage. Additionally, all patients underwent F-URSL successfully, and no statistically significant differences were observed between the two groups in terms of operative time, stone-free rates, postoperative fever, and postoperative hospital stay.

Conclusion
Both RUS and PCN have been established as effective approaches for managing urosepsis caused by upper urinary tract stones. Furthermore, the impact of these two drainage methods on the subsequent management of stones through elective F-URSL has shown consistent outcomes.
Comparison effects of Ferula gummosa essential oil and Beta-pinene Alginate nanoparticles on human melanoma and breast cancer cells proliferation and apoptotic index in short term normobaric hyperoxic model
Authors: Osanloo Mahmoud , Pishamad Somayyeh , ghanbariasad Ali , Zarenezhad Elham , Alipanah Media , Alipanah Hiva 
Published: November 2023

Abstract
Background
Breast cancer is the most common cancer among women, and melanoma is the most dreadful type of skin cancer. Due to the side effects of chemotherapy drugs, the development of new herbal nano-medicines has been considered.

Methods
This study first investigated the chemical composition of Ferula gummosa essential oil using GC-MS analysis; β-pinene, with 61.57%, was the major compound. Next, alginate nanoparticles containing β-pinene and the essential oil with particle sizes of 174 ± 7 and 137 ± 6 nm were prepared. Meanwhile, their zeta potentials were 12.4 ± 0.7 and 28.1 ± 1 mV. Besides, the successful loading of β-pinene and the essential oil in nanoparticles was confirmed using ATR-FTIR analysis. After that, their effects on viability and apoptotic index of human melanoma and breast cancer cells were investigated in normoxia and normobaric hyperoxia (NBO) conditions.

Results
The best efficacy on A-375 and MDA-MB-231 cells was achieved by alginate nanoparticles containing the EO at hyperoxic and normoxia conditions; IC50 76 and 104 µg/mL. Besides, it affected apoptosis-involved genes; as Bax/Bcl-2 ratio was higher than 1, conditions for induction of apoptosis were obtained. Higher sensitivity was observed in the A-375 cell line treated with Alg-EO in the NBO model.

Conclusions
Alginate nanoparticles containing F. gummosa EO could be considered for further investigation in anticancer studies. Also, it may be expected that NBO can be a new strategy for delaying cancer progression and improving nanotherapy efficacy.
A comparison between a maximum care university hospital and an outpatient clinic – potential for optimization in arthroscopic workflows?
Authors: Schenk Martin , Neumann Juliane , Adler Nadine , Trommer Tilo , Theopold Jan , Neumuth Thomas , Hepp Pierre 
Published: November 2023

Abstract
Background
Due to the growing economic pressure, there is an increasing interest in the optimization of operational processes within surgical operating rooms (ORs). Surgical departments are frequently dealing with limited resources, complex processes with unexpected events as well as constantly changing conditions. In order to use available resources efficiently, existing workflows and processes have to be analyzed and optimized continuously. Structural and procedural changes without prior data-driven analyses may impair the performance of the OR team and the overall efficiency of the department. The aim of this study is to develop an adaptable software toolset for surgical workflow analysis and perioperative process optimization in arthroscopic surgery.

Methods
In this study, the perioperative processes of arthroscopic interventions have been recorded and analyzed subsequently. A total of 53 arthroscopic operations were recorded at a maximum care university hospital (UH) and 66 arthroscopic operations were acquired at a special outpatient clinic (OC). The recording includes regular perioperative processes (i.a. patient positioning, skin incision, application of wound dressing) and disruptive influences on these processes (e.g. telephone calls, missing or defective instruments, etc.). For this purpose, a software tool was developed (‘s.w.an Suite Arthroscopic toolset’). Based on the data obtained, the processes of the maximum care provider and the special outpatient clinic have been analyzed in terms of performance measures (e.g. Closure-To-Incision-Time), efficiency (e.g. activity duration, OR resource utilization) as well as intra-process disturbances and then compared to one another.

Results
Despite many similar processes, the results revealed considerable differences in performance indices. The OC required significantly less time than UH for surgical preoperative (UH: 30:47 min, OC: 26:01 min) and postoperative phase (UH: 15:04 min, OC: 9:56 min) as well as changeover time (UH: 32:33 min, OC: 6:02 min). In addition, these phases result in the Closure-to-Incision-Time, which lasted longer at the UH (UH: 80:01 min, OC: 41:12 min).

Conclusion
The perioperative process organization, team collaboration, and the avoidance of disruptive factors had a considerable influence on the progress of the surgeries. Furthermore, differences in terms of staffing and spatial capacities could be identified. Based on the acquired process data (such as the duration for different surgical steps or the number of interfering events) and the comparison of different arthroscopic departments, approaches for perioperative process optimization to decrease the time of work steps and reduce disruptive influences were identified.
Clarity and adaptability of instructions preventing the spread of the COVID-19 virus and its association with individual and organisational factors regarding the psychosocial work environment: a cross-sectional study
Authors: Hammar Lena Marmstål , Alam Moudud , Eklund Caroline , Boström Anne-Marie , Lövenmark Annica 
Published: November 2023

Abstract
Background
In Sweden, older people in residential care had the highest mortality rates, followed by those who received home care, during the coronavirus disease 2019 (COVID-19) pandemic. Staff working in the care of older people assumed responsibility for preventing the spread of the virus despite lacking the prerequisites and training. This study aimed to investigate the psychosocial work environment during the COVID-19 pandemic among staff in the care of older people and examine the factors associated with staff’s perceptions of the clarity of instructions and the ability to follow them.

Methods
A cross-sectional study design was employed using a web survey. The staff’s perceptions of their psychosocial environment were analysed using descriptive statistics. The association between organisational and individual factors, as well as the degree of clarity of the instructions and the staff’s ability to follow them, were assessed using multivariate (ordinal) regression analysis.

Results
The main findings show that perceptions of the clarity and adaptability of the instructions were primarily correlated with organisational factors, as higher responses (positive) for the subscales focusing on role clarity, support and encouragement in leadership at work were associated with the belief that the instructions were clear. Similarly, those indicating high job demands and high individual learning demands were less likely to report that the instructions were clear. Regarding adaptability, high scores for demands on learning and psychological demands were correlated with lower adaptability, while high scores for role clarity, encouraging leadership and social support, were associated with higher adaptability.

Conclusions
High job demands and individual learning demands were demonstrated to decrease the staff’s understanding and adoption of instructions. These findings are significant on an organisational level since the work environment must be prepared for potential future pandemics to promote quality improvement and generally increase patient safety and staff health.
Calf morbidity, mortality, and management practices in dairy farms in Jimma City, Southwestern Ethiopia
Authors: Ahmedin Umer Mifta , Assen Alula Alemayehu 
Published: November 2023

AbstractBackgroundThis research aims to determine the incidence of calf morbidity, mortality and its potential predisposing factors in the first six months of life. Morbidity and mortality of dairy calves are persistent problems for dairy farmers worldwide. For effective control and prevention programs on calf health, it is imperative to estimate the extent of calf morbidity and mortality, and associated risk factors. Although few studies have investigated the epidemiology of calf morbidity and mortality in Ethiopia, comprehensive information is scarce in this area.MethodsData were collected through a cross-sectional survey and longitudinal follow-up on purposively selected dairy farms. A longitudinal study was conducted on 235 calves from birth to 6 months of age. Survival analysis methods using the Kaplan–Meier (K-M) method, and mixed effect Cox proportional hazard regression were employed to compute the life-to-event data on morbidity and mortality.ResultsFrom the 235 calves studied, 53 morbidity and 15 mortality events were recorded. This gives an overall morbidity and mortality incidence rate of 55 per 100-calf 6-months at risk (risk rate of 42.07%) and 14 per 100-calf 6-months at risk (risk rate of 12.97%), respectively. Diarrhea (13.84%) followed by pneumonia (8.97%) were the most common diseases that occurred in calves, respectively. Similarly, diarrhea (33.3%) and pneumonia (26.7%) were the leading causes of death. Dam parity (p < 0.001) and pen cleaning (p < 0.001) were significant predictors of calf morbidity. Dam parity (p = 0.007), calving status (p = 0.005), pen cleaning (p = 0.04), and floor type (p = 0.001) of houses were significantly associated with mortality. The hazard of diarrhea was significantly associated with sex (p = 0.003), first colostrum feeding time (p = 0.028), pen cleaning (p = 0.010), and breeding method (p = 0.013).ConclusionThe rates of morbidity and mortality reported in the study were higher than the economically acceptable, also affecting the welfare of the animals. The risk factors found need due attention in the management practices of dairy calves in Ethiopia.
Sulfate limitation increases specific plasmid DNA yield and productivity in E. coli fed-batch processes
Authors: Gotsmy Mathias , Strobl Florian , Weiß Florian , Gruber Petra , Kraus Barbara , Mairhofer Juergen , Zanghellini Jürgen 
Published: November 2023

AbstractPlasmid DNA (pDNA) is a key biotechnological product whose importance became apparent in the last years due to its role as a raw material in the messenger ribonucleic acid (mRNA) vaccine manufacturing process. In pharmaceutical production processes, cells need to grow in the defined medium in order to guarantee the highest standards of quality and repeatability. However, often these requirements result in low product titer, productivity, and yield. In this study, we used constraint-based metabolic modeling to optimize the average volumetric productivity of pDNA production in a fed-batch process. We identified a set of 13 nutrients in the growth medium that are essential for cell growth but not for pDNA replication. When these nutrients are depleted in the medium, cell growth is stalled and pDNA production is increased, raising the specific and volumetric yield and productivity. To exploit this effect we designed a three-stage process (1. batch, 2. fed-batch with cell growth, 3. fed-batch without cell growth). The transition between stage 2 and 3 is induced by sulfate starvation. Its onset can be easily controlled via the initial concentration of sulfate in the medium. We validated the decoupling behavior of sulfate and assessed pDNA quality attributes (supercoiled pDNA content) in E. coli with lab-scale bioreactor cultivations. The results showed an increase in supercoiled pDNA to biomass yield by 33% and an increase of supercoiled pDNA volumetric productivity by 13 % upon limitation of sulfate. In conclusion, even for routinely manufactured biotechnological products such as pDNA, simple changes in the growth medium can significantly improve the yield and quality.
Graphical Abstract
Comparison of deep learning-based image segmentation methods for intravascular ultrasound on retrospective and large image cohort study
Authors: Dong Liang , Lu Wei , Lu Xuzhou , Leng Xiaochang , Xiang Jianping , Li Changling 
Published: November 2023

AbstractObjectivesThe aim of this study was to investigate the generalization performance of deep learning segmentation models on a large cohort intravascular ultrasound (IVUS) image dataset over the lumen and external elastic membrane (EEM), and to assess the consistency and accuracy of automated IVUS quantitative measurement parameters.MethodsA total of 11,070 IVUS images from 113 patients and pullbacks were collected and annotated by cardiologists to train and test deep learning segmentation models. A comparison of five state of the art medical image segmentation models was performed by evaluating the segmentation of the lumen and EEM. Dice similarity coefficient (DSC), intersection over union (IoU) and Hausdorff distance (HD) were calculated for the overall and for subsets of different IVUS image categories. Further, the agreement between the IVUS quantitative measurement parameters calculated by automatic segmentation and those calculated by manual segmentation was evaluated. Finally, the segmentation performance of our model was also compared with previous studies.ResultsCENet achieved the best performance in DSC (0.958 for lumen, 0.921 for EEM) and IoU (0.975 for lumen, 0.951 for EEM) among all models, while Res-UNet was the best performer in HD (0.219 for lumen, 0.178 for EEM). The mean intraclass correlation coefficient (ICC) and Bland–Altman plot demonstrated the extremely strong agreement (0.855, 95% CI 0.822–0.887) between model's automatic prediction and manual measurements.ConclusionsDeep learning models based on large cohort image datasets were capable of achieving state of the art (SOTA) results in lumen and EEM segmentation. It can be used for IVUS clinical evaluation and achieve excellent agreement with clinicians on quantitative parameter measurements.
Identification and characterization of ARID1A-interacting proteins in renal tubular cells and their molecular regulation of angiogenesis
Authors: Yoodee Sunisa , Peerapen Paleerath , Plumworasawat Sirikanya , Malaitad Thanyalak , Thongboonkerd Visith 
Published: November 2023

Abstract
Background
Defects and deficiency of AT-rich interactive domain-containing protein 1A (ARID1A) encoded by a tumor suppressor gene ARID1A have recently been suggested to get involved in angiogenesis, a crucial process in carcinogenesis. However, molecular mechanisms of ARID1A deficiency to induce angiogenesis in kidney cancer remain underinvestigated.

Methods
We performed large-scale identification of ARID1A protein interactors in renal tubular epithelial cells (RTECs) using immunoprecipitation (IP) followed by nanoLC-ESI-LTQ-Orbitrap tandem mass spectrometry (MS/MS). Their roles in angiogenesis were investigated using various assays.

Results
A total of 74 ARID1A-interacting proteins were identified. Protein–protein interactions analysis revealed that these identified proteins interacted directly or indirectly with ARID1A. Among them, the direct interaction between ARID1A and β-actin was validated by IP and reciprocal IP followed by Western blotting. Small interfering RNA (siRNA) was used for single and double knockdowns of ARID1A and ACTB. Semi-quantitative RT-PCR demonstrated that deficiency of ARID1A, but not ACTB, significantly affected expression of angiogenesis-related genes in RTECs (VEGF and FGF2 were increased, whereas PDGF and EGF were decreased). However, the knockdowns did not affect TGFB1 and FGF1 levels. The quantitative mRNA expression data of VEGF and TGFB1 were consistent with the secreted levels of their protein products as measured by ELISA. Only secreted products derived from ARID1A-deficient RTECs significantly increased endothelial cells (ECs) migration and tube formation. Some of the other carcinogenic features could also be confirmed in the ARID1A-deficient RTECs, including increased cell migration and chemoresistance. Double knockdowns of both ARID1A and ACTB did not enhance the effects of single ARID1A knockdown in all assays.

Conclusions
We report herein a large dataset of the ARID1A-interacting proteins in RTECs using an IP-MS/MS approach and confirm the direct interaction between ARID1A and β-actin. However, the role of ARID1A deficiency in angiogenesis is independent of β-actin.