Miracle-dz/UniFAR-FTUs huggingface dataset:
A Machine Learning Approach to Predict the Outcome of Urinary Calculi Treatment Using Shock Wave Lithotripsy: Model Development and Validation Study

Background Shock wave lithotripsy (SWL), ureteroscopy, and percutaneous nephrolithotomy are established treatments for renal stones. Historically, SWL has been a predominant and commonly used procedure for treating upper tract renal stones smaller than 20 mm in diameter due to its noninvasive nature. However, the reported failure rate of SWL after one treatment session ranges from 30% to 89%. The failure rate can be reduced by identifying candidates likely to benefit from SWL and manage patients who are likely to fail SWL with other treatment modalities. This would enhance and optimize treatment results for SWL candidates. Objective We proposed to develop a machine learning model that can predict SWL outcomes to assist practitioners in the decision-making process when considering patients for stone treatment. Methods A data set including 58,349 SWL procedures performed during 31,569 patient visits for SWL to a single hospital between 1990 and 2016 was used to construct and validate the predictive model. The AdaBoost algorithm was applied to a data set with 17 predictive attributes related to patient demographics and stone characteristics, with success or failure as an outcome. The AdaBoost algorithm was also applied to a training data set. The generated model’s performance was compared to that of 5 other machine learning algorithms, namely C4.5 decision tree, naïve Bayes, Bayesian network, K-nearest neighbors, and multilayer perceptron. Results The developed model was validated with a testing data set and performed significantly better than the models generated by the other 5 predictive algorithms. The sensitivity and specificity of the model were 0.875 and 0.653, respectively, while its positive predictive value was 0.7159 and negative predictive value was 0.839. The C-statistics of the receiver operating characteristic (ROC) analysis was 0.843, which reflects an excellent test. Conclusions We have developed a rigorous machine learning model to assist physicians and decision-makers to choose patients with renal stones who are most likely to have successful SWL treatment based on their demographics and stone characteristics. The proposed machine learning model can assist physicians and decision-makers in planning for SWL treatment and allow for more effective use of limited health care resources and improve patient prognoses.
Decision uncertainty during hypothesis testing enhances memory accuracy for incidental information

Humans actively seek information to reduce uncertainty, providing insight on how our decisions causally affect the world. While we know that episodic memories can help support future goal-oriented behaviors, little is known about how hypothesis testing during exploration influences episodic memory. To investigate this question, we designed a hypothesis testing paradigm, in which participants figured out rules to unlock treasure chests. Using this paradigm, we characterized how hypothesis testing during exploration influenced memory for the contents of the treasure chests. We found that there was an inverted U-shaped relationship between decision uncertainty and memory, such that memory was best when decision uncertainty was moderate. An exploratory analysis also showed that surprising outcomes lead to lower memory confidence independent of accuracy. These findings support a model in which moderate decision uncertainty during hypothesis testing enhances incidental information encoding.
CLEC5a-directed bispecific antibody for effective cellular phagocytosis

ABSTRACT While antibody-dependent cellular phagocytosis mediated by activating Fcγ receptor is a key mechanism underlying many antibody drugs, their full therapeutic activities can be restricted by the inhibitory Fcγ receptor IIB (FcγRIIB). Here, we describe a bispecific antibody approach that harnesses phagocytic receptor CLEC5A (C-type Lectin Domain Containing 5A) to drive Fcγ receptor-independent phagocytosis, potentially circumventing the negative impact of FcγRIIB. First, we established the effectiveness of such an approach by constructing bispecific antibodies that simultaneously target CLEC5A and live B cells. Furthermore, we demonstrated its in vivo application for regulatory T cell depletion and subsequent tumor regression.
The Fab portion of immunoglobulin G has sites in the CL domain that interact with Fc gamma receptor IIIa

ABSTRACT The interaction between IgG and Fc gamma receptor IIIa (FcγRIIIa) is essential for mediating immune responses. Recent studies have shown that the antigen binding fragment (Fab) and Fc are involved in IgG-FcγRIII interactions. Here, we conducted bio-layer interferometry (BLI) and isothermal titration calorimetry to measure the kinetic and thermodynamic parameters that define the role of Fab in forming the IgG-FcγRIII complex using several marketed therapeutic antibodies. Moreover, hydrogen/deuterium exchange mass spectrometry (HDX-MS) and crosslinking mass spectrometry (XL-MS) were used to clarify the interaction sites and structural changes upon formation of these IgG-FcγRIII complexes. The results showed that Fab in IgG facilitates the interaction via slower dissociation and a larger enthalpy gain. However, a larger entropy loss led to only a marginal change in the equilibrium dissociation constant. Combined HDX-MS and XL-MS analysis revealed that the CL domain of Fab in IgG was in close proximity to FcγRIIIa, indicating that this domain specifically interacts with the extracellular membrane-distal domain (D1) and membrane-proximal domain (D2) of FcγRIIIa. Together with previous studies, these results demonstrate that IgG-FcγRIII interactions are predominantly mediated by the binding of Fc to D2, and the Fab-FcγRIII interaction stabilizes complex formation. These interaction schemes were essentially fucosylation-independent, with Fc-D2 interactions enhanced by afucosylation and the contribution of Fab slightly reduced. Furthermore, the influence of antigen binding on IgG-FcγRIII interactions was also investigated. Combined BLI and HDX-MS results indicate that structural alterations in Fab caused by antigen binding facilitate stabilization of IgG-FcγRIII interactions. This report provides a comprehensive understanding of the interaction between IgG and FcγRIII.
Jungian Epistemological Balance: A Framework for Conceptualizing Architectural Education?

Future designers will have to cope with rapidly changing, information-based, multicultural societies. Architectural educators do not agree on how to assist their students in preparing for those societies. This article describes current practices and values in architectural education, considers evidence that there have been substantial changes in those values over the last two decades, reviews two major societal trends that will affect future designers, proposes an intellectual framework for thinking about architectural education, and suggests ways in which that framework might be used to implement the needed changes in architectural education. The Issues ARCHITECTURAL PRACTICE IS CHANGING, AND IT IS WIDELY ACKNOWLedged that some corresponding changes in architectural education will be needed. Where consensus is lacking is on the issue of what changes in architectural education will best support our students' future needs. This paper proposes a framework-Jung's psychological types-within which architectural educators can conceptualize and assess both the needs of future designers and the
Demand and Application of Aero-spare Parts Based on Generalized Renewal Process

In view of the 6 types of performance failure rate of aerial equipment,we establish corresponding fault distribution models to meet and predict the demand of aero-spare parts.Considering the degree of repairing,we analyze the failure data by applying a generalized renewal process and estimate the parameter values of repair degree.We then calculate the average failure number of non-repairable and repairable parts in a Monte Carlo simulation.Finally we compare the results of perfect repair and general repair with an example.The presented method is more reasonable than previous ones with prospect of practical applications.
Program Synthesis of Sparse Algorithms for Wave Function and Energy Prediction in Grid-Based Quantum Simulations

We have recently shown how program synthesis (PS), or the concept of “self-writing code”, can generate novel algorithms that solve the vibrational Schrödinger equation, providing approximations to the allowed wave functions for bound, one-dimensional (1-D) potential energy surfaces (PESs). The resulting algorithms use a grid-based representation of the underlying wave function ψ(x) and PES V(x), providing codes which represent approximations to standard discrete variable representation (DVR) methods. In this Article, we show how this inductive PS strategy can be improved and modified to enable prediction of both vibrational wave functions and energy eigenvalues of representative model PESs (both 1-D and multidimensional). We show that PS can generate algorithms that offer some improvements in energy eigenvalue accuracy over standard DVR schemes; however, we also demonstrate that PS can identify accurate numerical methods that exhibit desirable computational features, such as employing very sparse (tridiagonal) matrices. The resulting PS-generated algorithms are initially developed and tested for 1-D vibrational eigenproblems, before solution of multidimensional problems is demonstrated; we find that our new PS-generated algorithms can reduce calculation times for grid-based eigenvector computation by an order of magnitude or more. More generally, with further development and optimization, we anticipate that PS-generated algorithms based on effective Hamiltonian approximations, such as those proposed here, could be useful in direct simulations of quantum dynamics via wave function propagation and evaluation of molecular electronic structure.
Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell–cell fusion, and neutralization sensitivity

ABSTRACT SARS-CoV-2 has caused the COVID-19 pandemic. B.1. 617 variants (including Kappa and Delta) have been transmitted rapidly in India. The transmissibility, pathogenicity, and neutralization characteristics of these variants have received considerable interest. In this study, 22 pseudotyped viruses were constructed for B.1. 617 variants and their corresponding single amino acid mutations. B.1. 617 variants did not exhibit significant enhanced infectivity in human cells, but mutations T478K and E484Q in the receptor binding domain led to enhanced infectivity in mouse ACE2-overexpressing cells. Furin activities were slightly increased against B.1. 617 variants and cell–cell fusion after infection of B.1. 617 variants were enhanced. Furthermore, B.1. 617 variants escaped neutralization by several mAbs, mainly because of mutations L452R, T478K, and E484Q in the receptor binding domain. The neutralization activities of sera from convalescent patients, inactivated vaccine-immunized volunteers, adenovirus vaccine-immunized volunteers, and SARS-CoV-2 immunized animals against pseudotyped B.1. 617 variants were reduced by approximately twofold, compared with the D614G variant.
Longitudinal associations between falls and future risk of cognitive decline, the Motoric Cognitive Risk syndrome and dementia: the Einstein Ageing Study

Abstract Background falls share risk factors with cognitive decline but whether falls predict cognitive decline, pre-dementia syndromes and dementia is poorly understood. Objectives this study aimed to examine if falls are associated with cognitive decline in specific domains and the risk of Motoric Cognitive Risk (MCR) syndrome and dementia. Design cross-sectional study. Methods in older people (age 80.6 ± 5.3 years) free of dementia at baseline, the number of falls (none, one or multiple) during the year before enrolment and the first year of follow-up (exposure) were recorded. Decline in specific cognitive functions (global cognition, episodic verbal memory, verbal fluency, working memory, response inhibition and processing speed-attention), incident MCR and incident dementia were outcome measures. Linear mixed effects models were used to examine the associations between falls and cognitive decline, adjusting for confounders. Cox proportional hazards models were used to determine if falls predicted risk of incident MCR or dementia. Results of 522 eligible participants, 140 had a single fall and 70 had multiple falls. Multiple falls were associated with a greater decline in global cognition, episodic memory, verbal fluency and processing speed-attention compared to those with no falls (P < 0.05). Over a median follow-up of 1.0 years 36 participants developed MCR and 43 participants developed dementia. Those with multiple falls had a two-fold increased risk of MCR compared to those with no falls, but no increased risk of developing dementia. Conclusions multiple falls may be an important marker to identify older people at greater risk of future cognitive decline and incident MCR.
The predictive value and correlation of β-catenin, CMTM6, and PD-L1 expression in colorectal cancer.

CMTM6 is a major regulator of PD-L1 expression. Aberrant WNT pathway signaling occurs in most sporadic colorectal cancers (CRC). However, the significance and correlation of β-catenin, CMTM6, and PD-L1 immunohistochemical expression in is CRC still unknown and need to be further verified. We evaluated the expression levels of β-catenin, CMTM6, PD-L1, and MMR (mismatch repair) proteins by immunohistochemistry in CRC tissue microarray (TMA), and evaluated the association among β-catenin, CMTM6, PD-L1 expression, MMR status, and clinicopathological features in 704 CRC patients. Positive expression of PD-L1 in tumor cells (TC) is associated with more frequent dMMR (mismatch repair deficient) status, CMTM6 expression, right colon, and younger CRC patients. The expression of PD-L1 in tumor-infiltrating immune cells (IC) is associated with a higher frequency of adenocarcinoma, β-catenin, and CMTM6 expression. In univariate analysis, age, histological subtype, histologic grade, lymphatic metastasis, TNM stage, MMR status, and expression of PD-L1 protein in IC were significantly associated with the overall survival. In multivariate analysis, age, histologic grade, TNM stage, MMR status, and expression of PD-L1 protein in IC were independent prognostic factors. The overall survival of the adjuvant chemotherapy group was significantly higher than those non-chemotherapy in TNM stage III-IV CRC patients, but no significant overall survival improvement was found in the positive PD-L1 in TC, positive PD-L1 in IC, positive CMTM6, low β-catenin expression, or dMMR status subgroups. Expression of CMTM6 and PD-L1 in CRC are positively associated with β-catenin and reliable biomarkers for the prediction of responding to chemotherapy. The expression of β-catenin/CMTM6/PD-L1 and MMR status may be valuable biomarkers for guiding different treatment strategies in CRC patients.
When Poly(A) Binding Proteins Meet Viral Infections, Including SARS-CoV-2

Viruses have evolved diverse strategies to hijack the cellular gene expression system for their replication. The poly(A) binding proteins (PABPs), a family of critical gene expression factors, are viruses’ common targets. ABSTRACT Viruses have evolved diverse strategies to hijack the cellular gene expression system for their replication. The poly(A) binding proteins (PABPs), a family of critical gene expression factors, are viruses’ common targets. PABPs act not only as a translation factor but also as a key factor of mRNA metabolism. During viral infections, the activities of PABPs are manipulated by various viruses, subverting the host translation machinery or evading the cellular antiviral defense mechanism. Viruses harness PABPs by modifying their stability, complex formation with other translation initiation factors, or subcellular localization to promote viral mRNAs translation while shutting off or competing with host protein synthesis. For the past decade, many studies have demonstrated the PABPs’ roles during viral infection. This review summarizes a comprehensive perspective of PABPs’ roles during viral infection and how viruses evade host antiviral defense through the manipulations of PABPs.
Draft Genome Sequence of Thermoactinomyces vulgaris Strain AGRTWHS02, Isolated from Pasture Soil of a Sheep Dairy Farm in New Zealand

Thermoactinomyces species are heat-resistant spore-forming bacteria that are capable of producing proteases. Here, we report the draft genome sequence of a new Thermoactinomyces vulgaris strain, AGRTWHS02, with a strong proteolytic activity, which was isolated from a sheep dairy farm environment in New Zealand. The genome is 2.56 Mbp, with a GC content of 47.9%. ABSTRACT Thermoactinomyces species are heat-resistant spore-forming bacteria that are capable of producing proteases. Here, we report the draft genome sequence of a new Thermoactinomyces vulgaris strain, AGRTWHS02, with a strong proteolytic activity, which was isolated from a sheep dairy farm environment in New Zealand. The genome is 2.56 Mbp, with a GC content of 47.9%.
Frontal QRS-T angle may predict reverse dipping pattern in masked hypertensives

ABSTRACT Aims The frontal QRS-T (fQRST) angle is associated with worse cardiovascular outcome. The study aimed to assess the effect of reverse dipping pattern on f(QRST) angle in newly diagnosed masked hypertensive (MH) patients. Materials and methods Newly diagnosed 244 consecutive MH patients were included. According to dipping pattern, patients were grouped into three: dipper (n = 114), non-dipper (n = 106), and reverse dipper (n = 24) patterns. The f(QRST) angle, QT and corrected QT interval, and QT dispersion were measured from the 12-lead surface electrocardiogram and compared between groups. Results Of all, 51.2% (n = 125) were male. No gender difference was observed. Reverse dipper MH group had a significantly higher f(QRST) angle than the non-dipper and dipper MH groups (77.9 ± 8.6 vs. 32.4 ± 18.8 and 26.0 ± 18.5, respectively, p < .001). The cutoff value for f(QRST) angle of 51 predicts reverse dipping pattern (AUC: 0.84; 95% CI: 0.77–0.90; p < .001), with a sensitivity of 83% and a specificity of 78%. Conclusion This study revealed that f(QRST) angle is gradually increased starting from the dipper, non-dipper to reverse dipper masked hypertensives. The f(QRST) angle appears as an easy marker for the detection and risk stratification of hypertensive patients.
Tree species diversity increases with conspecific negative density dependence across an elevation gradient.

Elevational and latitudinal gradients in species diversity may be mediated by biotic interactions that cause density-dependent effects of conspecifics on survival or growth to differ from effects of heterospecifics (i.e. conspecific density dependence), but limited evidence exists to support this. We tested the hypothesis that conspecific density dependence varies with elevation using over 40 years of data on tree survival and growth from 23 old-growth temperate forest stands across a 1,000-m elevation gradient. We found that conspecific-density-dependent effects on survival of small-to-intermediate-sized focal trees were negative in lower elevation, higher diversity forest stands typically characterised by warmer temperatures and greater relative humidity. Conspecific-density-dependent effects on survival were less negative in higher elevation stands and ridges than in lower elevation stands and valley bottoms for small-to-intermediate-sized trees, but were neutral for larger trees across elevations. Conspecific-density-dependent effects on growth were negative across all tree size classes and elevations. These findings reveal fundamental differences in biotic interactions that may contribute to relationships between species diversity, elevation and climate.
Maternal long working hours and offspring's weight‐related outcomes: A systematic review and meta‐analysis

It is unclear whether maternal working time has an impact on offspring's weight‐related outcomes especially obesity; the objective of this study is to conduct the first meta‐analysis to focus on this topic. We searched PubMed, Ovid, and Web of Science databases through August 2021. A random‐effect model was used to assess the pooled odds ratios (ORs) and regression coefficients (β) with their corresponding 95% confidence intervals (95% CIs). Subgroup analyses were conducted to explore sources of heterogeneity. Publication bias was evaluated by the Egger's tests. Twenty‐two observational studies were included with a total of 191,420 participants. Compared with children whose mothers worked less than 35 h/week, we found that children whose mothers worked more than 35 to 40 h/week had a 2.24‐fold increased risk of childhood overweight/obesity (OR = 2.24, 95% CI: 1.61–3.11). An increment of 10 h/week in maternal working was associated with an approximately 1.0 percentage points in the probability of childhood overweight/obesity (β = 0.008, 95% CI: 0.004–0.012). The pooled OR also indicated a similar result (OR = 1.09, 95% CI: 1.04–1.15). In addition, an increment of 10 h/week in maternal working was associated with 0.029 units increase in offspring's BMI z score (β = 0.029, 95% CI: 0.016–0.042). Maternal long working hours is a potential risk factor for offspring's weight‐related outcomes. Measures should be taken to protect the work welfare of females, thus facilitating the positive interaction of individual–family–society.