bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving AlphaFold2-based Protein Tertiary Structure Prediction with MULTICOM in CASP15
Authors: Liu Jian , Guo Zhiye , Wu Tianqi , Roy Raj , Chen Chen , Cheng Jianlin 
Published: June 2023

Abstract
Since demonstrating its outstanding performance in the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14) in 2020, AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge in the field is to further improve the accuracy of AlphaFold2-based protein structure prediction. To address this challenge, we developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are further refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure prediction together to account for tertiary structural changes induced by protein-protein interaction in the assembly. The MULTICOM system participated in the tertiary structure prediction in 2022 CASP15 experiment as server and human predictors. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% and higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively. The results demonstrate that our approach can significantly improve the accuracy of the AlphaFold2-based protein tertiary structure prediction.
Human equivalent doses of L-DOPA rescues retinal morphology and visual function in a murine model of albinism
Authors: Sanchez-Bretano Aida , Keeling Eloise , Scott Jennifer A. , Lynn Savannah A. , Soundara-Pandi Sudha Priya , Macdonald Sarah L. , Newall Tutte , Griffiths Helen , Lotery Andrew J. , Ratnayaka J. Arjuna , Self Jay E. , Lee Helena 
Published: June 2023

Abstract
L-DOPA is deficient in the developing albino eye, resulting in abnormalities of retinal development and visual impairment. Ongoing retinal development after birth has also been demonstrated in the developing albino eye offering a potential therapeutic window in humans. To study whether human equivalent doses of L-DOPA/Carbidopa administered during the crucial postnatal period of neuroplasticity can rescue visual function, OCA C57BL/6J-c2J OCA1 mice were treated with a 28-day course of oral L-DOPA/Carbidopa at 3 different doses from 15 to 43 days postnatal age (PNA) and for 3 different lengths of treatment, to identify optimum dosage and treatment length. Visual electrophysiology, acuity, and retinal morphology were measured at 4, 5, 6, 12 and 16 weeks PNA and compared to untreated C57BL/6J (WT) and OCA1 mice. Quantification of PEDF, βIII-tubulin and syntaxin-3 expression was also performed. Ourdata showed impaired retinal morphology, decreased retinal function and lower visual acuity in untreated OCA1 micecompared to WT mice. These changes were diminished or eliminated when treated with higher doses of L-DOPA/Carbidopa. Our results demonstrate that oral L-DOPA/Carbidopa supplementation at human equivalent doses during the postnatal critical period of retinal neuroplasticity can rescue visual retinal morphology and retinal function, via PEDF upregulation and modulation of retinal synaptogenesis, providing a further step towards developing an effective treatment for albinism patients.
Title: Does progesterone as predictive for a successful pregnancy along all age groups in fresh IVF/ICSI transfer cycles?
Authors: Ip Patricia Nga Ping , Fung Ka Kei , CHUNG Jacqueline Pui Wah , Zhao Mingpeng , Chan David Yiu Leung 
Published: June 2023

Abstract
Background
Meta-analyses have shown that progesterone (P) elevation is associated with a decreased probability of pregnancy achievement in fresh in vitro fertilization (IVF) cycles. The objective of this study is to evaluate the P level, the P to oocyte ratio (P/O) and the P to follicle (> 14 mm) ratio (P/F) in prediction of successful pregnancy in different age groups.
Methods
This was a retrospective, single-centre cohort study with 1517 cycles performed in 1305 patients undergoing controlled ovarian stimulation and fresh embryo transfer cycles between 2015 and 2021. We investigated the association of serum progesterone level on the day of ovulation trigger with live birth among patients age ≤ 35 (group 1), 36–39 (group 2) and ≥ 40 (group 3).
Results
The progesterone level was significantly associated with the live birth rate in group 1 (aOR 0.422, 95% CI 0.231–0.770, p = 0.005), but not in group 2 (aOR 0.626, 95% CI 0.362–1.084, p = 0.095) and group 3 (aOR 0.311, 95% CI 0.042–2.284, p = 0.251). The live birth rate was significantly reduced in group 1 with P > 1.00 ng/mL (36.8% vs. 23.6%, p = 0.002). No significant difference in the live birth rate was found with P > 1.00 ng/mL in both groups 2 and 3. Both the P/O and P/F ratios, though were more predictive than P alone in live birth rate among all age groups, the values increased substantially with age.
Conclusions
Our results suggest that progesterone elevation is less predictive to live birth rate among patients age above 35. While the P/O or P/F ratio are significantly higher among women without live birth in all 3 age groups, their age-dependent values suggest the definition of a universal threshold should be warranted.
Relationship between coping styles and affective decision- making process among schizophrenia patients and healthy controls
Authors: Kertzman Semion , Rauchverger Boris , Waseem Shiech Zaid , Weizman Abraham , Portuguese Shirley , Grinshpoon Alexander 
Published: June 2023

Abstract
Psychiatry has shown a growing interest in the role of emotion in decision- making because emotion appears to make a substantial contribution to the decision- making process. There are no studies analyzing the relationship between affective decision-making and coping skills in schizophrenia (SZ). Our objective was to investigate the effect of coping skills on decision-making in SZ. We aimed to study the differences in coping styles, measured by the Behavioral Attitudes and Search Evaluation test (BASE), between good and bad performers on the Iowa Gambling Task (IGT). The 37 SZ participants and 46 healthy controls (HC) performed the IGT and BASE. Affective decision-making and coping skills are impaired among individuals with SZ compared with HC. A combination of two coping styles, such as preference for search activity and rejection of renunciation of search, was associated with better performance on IGT in both groups. We demonstrate that the association between coping style and performance on the IGT is not bidirectional. Coping strategies affect IGT performance, while performance on IGT does not affect coping style. In conclusion, participants with a more adaptive coping style were better decision-makers. One possible explanation for this association is that the more effective coping style may represent better functioning of the affective systems.
Digitalization-A Strategic Approach to Promote Garage and Vehicle Services in order to provide effective services in Sri Lanka
Authors: N.A.R Udeshi , R.D.A Shehara , H Weerasinghe , T.D Gajasinghe , De Silva D. I. , H.M.P.P.K.H Samarasekara 
Published: June 2023

Abstract
This web application aims to provide a seamless platform for vehicle owners to locate and book available garage services, and fuel station services, buy available products by visiting shops and get insurance companies according to related features with ease. The application will feature a user-friendly interface that will enable users to browse and compare prices, ratings, and product details offered by different shops. The application will also have a scheduling system for garages that will allow users to book appointments, receive notifications and track the status of their vehicle repairs. This web application is designed to help users locate fuel stations, shops, and garages near their current location quickly and easily. Customers can easily browse and compare insurance plans according to features companies provide directly through the website. Additionally, the application will offer feedback mechanisms to ensure customer satisfaction. The web application aims to simplify the process of maintaining and repairing vehicles while promoting transparency, reliability, and convenience.
Starting-Accessibility / Water Internal Diffusion (SAWID) Phenomenological Model of Myrtle Drying Kinetics
Authors: Berrich oumaima , Allaf Karim , Azzouz Soufien , Besombes Colette , Hamrouni Lamia 
Published: June 2023

Abstract
To avoid empirical modeling and embrace a relevant phenomenological analysis, the present work deals with the conditions allowing to adopt the transfer by internal water diffusion as the limiting process of the whole drying. Verification of the Negligible External Resistance NER criterion has been conducted and the main part of the drying kinetics allows expressing the effective diffusivity Deff of water within the porous material. Moreover, the kinetic experimental data of both the initial and final stages must be excluded. The first one concerns the surface interaction while the last paradoxical stage reveals the vapor transfer within the porous medium. Instant Controlled Pressure-Drop DIC pretreatment was adopted in the drying of myrtle leaves and fruits. An instant pressure drop towards a vacuum occurs after a saturated steam pressure P ranged between 100 and 500 kPa for a short processing time tof20/60s and 10/30 s for myrtle leaves and fruits, respectively. Afterward, the drying experiments were carried out with a constant airflow of 50°C and 2.5 m/s. The phenomenological modeling of drying kinetics was dedicated to well analyzing the impact of DIC operating parameters on the physical and statistical analyses.
Early cumulus cell removal increases cumulative live birth rate while having no negative effect on the malformation rate in in vitro fertilization: a propensity score-matched cohort study
Authors: Sun Li Juan , Liang Shan Shan , Liu Min Hao , Pan Jia Ping , Huang Mei Yuan , Teng Xiao Ming , wu Hai Xia 
Published: June 2023

Abstract
Purpose
The aim of this study was to investigate the efficacy and safety of early cumulus cell removal (ECCR) during human in vitro fertilization (IVF).
Methods
A retrospective analysis was performed between January 2011 and December 2019. The study enrolled 1,131 couples who underwent IVF treatment with ECCR. After propensity score matching at a 1:1 ratio, 1,131 couples who underwent overnight coincubation of gametes were selected. The main outcome measure was the cumulative live birth rate. Secondary outcome measures included the cumulative pregnancy rate, polyspermy rate, available embryo rate, miscarriage rate, malformation rate, time to live birth, and oocyte-to-baby rate.
Results
There were no significant differences found between the two groups in the polyspermy rate, available embryo rate, miscarriage rate, time to live birth, oocyte-to-baby rate, and neonatal congenital anomalies rate. The results of the study showed that ECCR was associated with a significantly higher cumulative live birth rate and cumulative pregnancy rate, along with a significantly lower fertilization rate.
Conclusion
ECCR tended to confer increased cumulative live birth rate and had no negative effect on the neonatal malformation rate.
The associations of natural killer cell functions during the embryo implantation window with pregnancy outcomes in women for whom the number of peripheral blood natural killer cells cannot be applied as a therapeutic index for immunological abnormalities in unexplained recurrent pregnancy loss
Authors: YAN Niwei , LEE Pingyin , JIE Huiying , YUAN Yuan , ZHOU Canquan 
Published: June 2023

Abstract
Study objective The current knowledge on recurrent pregnancy loss (RPL) is largely limited, with up to 70% of RPL cases still classified as unexplained. More than 30% of patients with unexplained recurrent pregnancy loss (uRPL) will suffer an additional pregnancy loss. The majority of scholars are supportive of an immune basis, while clinical data fail to support established therapies. In addition, the effectiveness of immunotherapies is difficult to evaluate because of the lack of diagnostic and predictive indicators. Natural Killer (NK) cells are the largest population of lymphocytes in the endometrium during early pregnancy and play a key regulatory rather than participatory role in the cytotoxic killing reaction to embryos at the maternal-fetal interface. Specifically, they support the invasion of trophoblast cells and embryo implantation. Previous studies on the roles of NK cells with distinct phenotypes in pregnancy loss were based on NK cells derived from the peripheral blood or decidua, and it is difficult to determine whether the reported changes in decidual NK cells are causes or consequences of pregnancy loss. Hence, whether the results of these studies are applicable to the interaction between NK cells and embryonic trophoblast cells during the earliest pregnancy stage remains unknown.Design This study evaluated the expression of 9 receptors and cytokines after coculture of the HTR-8/SVneo human chorionic trophoblast cell line with peripheral blood NK (pbNK) cells and uterine NK (uNK) cells collected during the same embryo implantation window. Then the phenotypes of NK cells during this period were analyzed, and the associations of NK cell functional features with early pregnancy outcomes were explored.Results We found that a decrease in the CD3-CD56 + CD27 + uNK cell population and increases in the frequencies of CD3-CD56 + CD107a + NK cells in women with the recurrence of pregnancy loss.Conclusions CD3-CD56 + IFN-γ + pbNK cells and CD3-CD56 + IFN-γ + uNK cells were immunological risk factors associated with the recurrence of pregnancy loss in uRPL.
Economic Burden of Sanfilippo Syndrome in the United States
Authors: Ashby Frederick , Park Haesuk , Svensson Mikael , Heldermon Coy 
Published: June 2023

Abstract
Introduction: Sanfilippo syndrome is a rare disease and fatal genetic disorder in the United States with no FDA-approved treatment, and no comprehensive assessment of economic disease burden is available.Objective To develop a model to estimate the economic burden associated with Sanfilippo syndrome in the United States (US) using valued intangibles (disability-adjusted life years lost) and indirect burden (lost caregiver productivity) from 2023 onward.Design and Setting: A multistage comorbidity model was generated using publicly available literature on Sanfilippo syndrome disability, and 14 disability weights from the 2010 Global Burden of Disease Study. Attributable increase in caregiver mental health burden and caregiver productivity loss were also estimated using data from the CDC National Comorbidity Survey, retrospective studies on caregiver burden in Sanfilippo syndrome, and the Bureau of Labor Statistics. Monetary valuations were adjusted to USD 2023 and given a 3% discount rate from 2023 onward.Main Outcomes and Measures: Year-over-year incidence and prevalence of Sanfilippo syndrome was calculated for each age group in each year, and year-over-year disability-adjust life years (DALYs) lost due to patient disability was calculated by comparing to health-adjusted life expectancy (HALE), considering years of life lost (YLLs) due to premature mortality and years lived with disability (YLDs). Intangibles were valued in USD 2023, adjusted for inflation and discounted to provide economic burden of disease.Results From 2023–2043, overall economic burden in the US attributable to Sanfilippo syndrome was estimated to be $1.55 billion USD with current standard of care. The burden to individual families exceeded $5.86 million present value from time of birth per child born with Sanfilippo syndrome. These figures are also a conservative estimate, since they do not consider direct cost associated with the disease, as extensive primary data on the direct healthcare cost of Sanfilippo syndrome does not currently exist in the literature.Conclusions and Relevance: Sanfilippo syndrome is a rare lysosomal storage disease, however the severe burden associated with the disease for individual families demonstrates a profound cumulative impact. Our model represents the first disease burden estimate associated with Sanfilippo syndrome. This underscores the substantial morbidity and mortality burden of Sanfilippo syndrome.
Effects of Cell Phone Presence on the Control of Visual Attention During the Navon Task
Authors: Liu Wenjuan , Kawashima Tomoya , Shinohara Kazumitsu 
Published: June 2023

Abstract
Background
Although cell phones can provide great convenience to our lives, research has shown that they can also affect our behavior, even when not in use. It seems that having a cell phone nearby may not be ideal when the user needs to concentrate on work. However, little is known about whether cell phone presence specifically impairs attentional control.
Methods
This study investigated whether cell phone presence can influence attentional control in the Navon task, which involves spatial switching of attention between global and local levels.
Results
It was found that the reaction time for all types of trials decreased when the participants had a cell phone nearby compared to when they had a mobile battery nearby. It was also found that phone dependency led to more incorrect responses among participants, but this effect was independent of the influence of phone presence on the Navon task performance.
Conclusions
These findings indicated that cell phone presence may have a positive influence on the perceptual process of the Navon letter, suggesting that the effects of phone presence are not always negative.
Research on Milling Chatter Monitoring and Suppression Based on IWPEE and VASS Dual Indicators
Authors: Li Xudong , Huang Hua , Zhao Conglin , Nie Xingyi 
Published: June 2023

Abstract
Chatter is harmful for cutting processing, which can cause the surface quality of the workpiece to decline, violent tool wear, even broken tools and workpiece scrap. In order to achieve real-time monitoring and suppression of chatter during the machining process, a milling machining is employed as the research object in this study, and an online monitoring and suppression system for chatter is proposed. Firstly, an improved wavelet packet energy entropy(IWPEE) algorithm is proposed, the recognition accuracy and robustness is improved by this algorithm while the computational complexity is reduced. Secondly, in order to ensure the robustness of the monitoring system in practical application, a variance algorithm for the milling signal sampling is synchronized with the spindle speed(VASS) is proposed by analyzing milling cutter motion through Poincare section. In addition, the position of the spindle rotation is indirectly obtained through mathematical calculations, the signal sampling is ensured synchronized with the spindle rotation period, and the sensors are not necessary so the generalization besides economy is improved. Furthermore, VASS overcomes the defects of IPWEE which is vulnerable to high-frequency noise interference, thereby improving the reliability of chatter monitoring. Then, a dynamic modeling of the cutting system is conducted, and a chatter suppression method based on speed iteration is obtained. Finally, the effectiveness of the proposed chatter monitoring and suppression system is verified through milling experiments.
Graphene/polyacrylamide interpenetrating structure hydrogels for wastewater treatment
Authors: Zhu Xiufang , Wang Zelin , Ren Jian , Zhang Chun , Zhang Jun , Zhou Juying , Li Mufang , Wang Dong , Seok Ilwoo , Guo Xingkui 
Published: June 2023

Abstract
Acrylamide (AM) was used as the initial reaction monomer, N,N-methylene bisacrylamide (MBA) was used as the crosslinking agent, and ammonium persulfate (APS) was used as the initiator to prepare the first network structure. Graphene oxide (GO) aqueous solution was dispersed after heating and reacted with tannic acid (TA) to generate the interpenetrating network structure (IPN). The hydrogel composite was characterized by the Fourier transform infrared, ultraviolet spectrum techniques and scanning electron microscopy to analyze structural characteristics and adsorption interactions. Thermodynamic investigation explored the nature that adding GO into the hydrogel, the thermogravimetric temperature increases with the amount of GO. The reaction kinetics was essentially consistent with the pseudo-second-order model with rate dominated by the intraparticle diffusion model as well as the film diffusion mechanism. The water absorption in the equilibrium state was about 300%, better sorption capacity (110.25 mg/g for nickel chloride).
Cardiac Protective Techniques in Left Breast Radiotherapy: Rapid selection criteria for routine clinical decision making
Authors: Bolukbas Meltem Kirli , Karaca Sibel , Coskun Volkan , Uzel Esengul Kocak 
Published: June 2023

Abstract
Objective: In left breast radiotherapy (RT) desired heart doses may be achieved without heart-sparing RT techniques in some patients. We aimed to examine the existence of predictive factors and cut-off points to determine which patients are the main candidates for heart-sparing RT techniques.
Material and method: Dosimetric data for left breast cancer was examined. RT plans were made at conventional doses to the breast and peripheral lymph nodes. Statistical analyzes were performed using SPSS 22.0 (SPSS Inc.,IBM Corp.,Armonk, NY).
Results: 114 cases were evaluated by ROC analysis in the breast conserving surgery (BCS) and mastectomy groups. While only left lung volume (AUC:0.74, 95%CI:0.61-0.87, p=0.002) was significant in BCS cases, in cases with mastectomy, left lung volume (AUC:0.81, 95%CI:0.69-0.94, p=0.002) and lung/heart volume ratio (AUC:0.83,95%CI:0.70-0.96, p=0.001) had a significant relationship with the relevance of heart doses. The cut-off point of 1.92 was selected for the lung/heart volume ratio for the mastectomized patients. Moreover, the cut-off point 1154 cc and 1208 cc was determined for the left lung volume for the BCS and mastectomized patients, respectively.
Conclusion: Various cut-off points in left breast RT can be used to predict whether RT plans will meet QUANTEC heart dose limits. Evaluating only these few cut-off points before planning makes it possible to eliminate 70% of patients with BCS and 40% of patients with mastectomy from respiratory-controlled methods, which require time and effort. Patients with lung volume and lung/heart volume ratio smaller than the cut-off values can be considered primary candidates for heart-sparing techniques.