Miracle-dz/UniFAR-FTUs huggingface dataset:
More than just pattern recognition: Prediction of uncommon protein structure features by AI methods

Significance Generalization from the training data is a test of a true AI. Methods for computing protein structure using AI have been criticized as merely using pattern recognition rather than knowledge of the rules of physics and chemistry. Here, we show that contrary to this view, AI methods can accurately identify rarely observed features in crystal structures, provided these are not induced by the crystal environment. In contrast, pattern recognition would usually select the more commonly observed structural feature. We propose that in this application, the AI network has learned the principles of protein structure such that it can successfully apply those to previously unobserved situations.
Comprehensive Analysis of Individual Anatomical Structures for Micturition Symptoms and Maximum Flow Rate in Men With Benign Prostatic Hyperplasia/Lower Urinary Tract Symptoms

Purpose Individual anatomical structural variations, including intravesical prostatic protrusion (IPP), prostatic urethral angle (PUA), prostatic urethral length, or prostatic apex shape, were correlated with micturition symptoms. We aimed to investigate the effects of these variables on micturition symptoms in men with benign prostatic hyperplasia (BPH)/lower urinary tract symptoms (LUTS). Methods This observational study was based on data from 263 men with the first visit to health promotion center and without BPH/LUTS treatment between March 2020 and September 2022. A multivariate analysis was performed to determine the variables affecting total international prostate symptom score, maximum flow rate (Qmax), and voiding efficacy (postvoid residual volume to total bladder volume ratio). Results Of 263 patients, decreasing PUA increases the severity of international prostate symptoms score (mild, 141.9°; moderate, 136.0°; severe, 131.2°; P<0.015). A multivariate analysis reported that the total international prostate symptom score was correlated with age (P=0.002), PUA (P=0.007), and Qmax (P=0.008). Qmax was negatively associated with IPP (P=0.002). In subanalysis for large prostate volume (≥30 mL, n=81), international prostate symptom score was correlated with PUA (P=0.013), Qmax was correlated with prostatic apex shape (P=0.017), and length of proximal prostatic urethra (P=0.007). IPP was not identified as a significant factor. For small prostate volume (<30 mL, n=182), age (P=0.011) and prostate volume (P=0.004) are correlated with increasing Qmax. Conclusions This study presented that individual anatomical structure variations influenced the micturition symptoms according to prostate volume. To identify the major resistant factors in men with BPH/LUTS, further studies are required to investigate which components played a role in major resistant factors for micturition symptoms.
The HDAC2–MTA3 interaction induces nonsmall cell lung cancer cell migration and invasion by targeting c‐Myc and cyclin D1

Genome‐wide association studies have identified numerous single‐nucleotide polymorphisms (SNPs) associated with lung cancer; however, the functions of histone deacetylase 2 (HDAC2) rs13213007 and HDAC2 in nonsmall cell lung cancer (NSCLC) remain unclear. Here we identified HDAC2 rs13213007 as a risk SNP and showed that HDAC2 was upregulated in both peripheral blood mononuclear cells (PBMCs) and NSCLC tissues with the rs13213007 A/A genotype compared with those with the rs13213007 G/G or G/A genotype. Patient clinical data indicated strong associations between rs13213007 genotype and N classification. Immunohistochemical staining confirmed that higher expression of HDAC2 was associated with NSCLC progression. Furthermore, we generated 293T cells with the rs13213007 A/A genotype using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 gene editing. Chromatin immunoprecipitation sequencing followed by motif analysis showed that HDAC2 can bind to c‐Myc in rs13213007 A/A 293T cells. Cell Counting Kit‐8, colony formation, wound‐healing, and Transwell assays revealed that HDAC2 upregulates c‐Myc and cyclin D1 expression and promotes NSCLC cell proliferation, migration, and invasion. Co‐immunoprecipitation, quantitative reverse transcription–polymerase chain reaction, and western blot analysis assays showed that MTA3 interacts with HDAC2, decreases HDAC2 expression, and rescues the migration and invasion abilities of NSCLC cells. Taken together, these findings identify HDAC2 as a potential therapeutic biomarker in NSCLC.
A Landau‐Lifshitz‐Gilbert‐Type equation and torsion effects on the dynamics of magnetization

Based on the non‐relativistic regime of electrons described by a Dirac equation coupled to a torsion pseudo‐vector, we study the dynamics of magnetization and how it may be affected by the presence of this (background) torsion field. The latter describes some anisotropy of the bulk and it may be accounted for in two ways: by means of a minimal coupling in a covariant derivative endowed with spin connection and a gauge magnetic field; in addition, through a non‐minimal interaction term with the spin density. We show, within this framework, that it is possible to attain a version of the Landau‐Lifshitz equation in presence of the torsion background where its effects are included, re‐enforcing that torsion corresponds to a geometric anisotropy with relevant unfolds on the spin coupling mechanism. We also conclude that the torsion terms can open up two important landscapes in the magnetization dynamics: one of them, related with a damping effect; the other, related with the screw dislocation that gives us a global effect like a sharped‐helix damping. The whole effort here is then to pursue an investigation of torsion in connection with the precession dynamics of the magnetization.
Wafer-scale striped network transistors based on purified semiconducting carbon nanotubes for commercialization

Highly purified and solution-processed semiconducting carbon nanotubes (s-CNTs) have developed rapidly over the past several decades and are near-commercially available materials that can replace silicon due to its large-area substrate deposition and room-temperature processing compatibility. However, the more s-CNTs are purified, the better their electrical performance, but considerable effort and long centrifugation time are required, which can limit commercialization due to high manufacturing costs. In this work, we therefore fabricated ‘striped’ CNT network transistor across industry-standard 8 inch wafers. The stripe-structured channel is effective in lowering the manufacturing cost because it can maintain good device performance without requiring high-purity s-CNTs. We evaluated the electrical performances and their uniformity by demonstrating striped CNT network transistors fabricating from various s-CNT solutions (e.g. 99%, 95%, and 90%) in 8 inch wafers. From our results, we concluded that by optimizing the CNT network configurations, CNTs can be sufficiently utilized for commercialization technology even at low semiconducting purity. Our approach can serve as a critical foundation for future low-cost commercial CNT electronics.
Defining bone fide effectors of RAS GTPases

RAS GTPases play essential roles in normal development and are direct drivers of human cancers. Three decades of study have failed to wholly characterize pathways stimulated by activated RAS, driven by engagement with ‘effector’ proteins that have RAS binding domains (RBDs). Bone fide effectors must bind directly to RAS GTPases in a nucleotide‐dependent manner, and this interaction must impart a clear change in effector activity. Despite this, for most proteins currently deemed effectors there is little mechanistic understanding of how binding to the GTPase alters protein function. There has also been limited effort to comprehensively resolve the specificity of effector binding to the full array of RAS superfamily GTPase proteins. This review will summarize what is known about RAS‐driven activation for an array of potential effector proteins, focusing on structural and mechanistic effects and highlighting how little is still known regarding this key paradigm of cellular signal transduction.
Frequency-Dependent F-Number Suppresses Grating Lobes and Improves the Lateral Resolution in Coherent Plane-Wave Compounding

Ultrafast imaging modes, such as coherent plane-wave compounding (CPWC), increase image uniformity and reduce grating lobe artifacts by dynamic receive apertures. The focal length and the desired aperture width maintain a given ratio, which is called the <inline-formula> <tex-math notation="LaTeX">${F}$ </tex-math></inline-formula>-number. Fixed <inline-formula> <tex-math notation="LaTeX">${F}$ </tex-math></inline-formula>-numbers, however, exclude useful low-frequency components from the focusing and reduce the lateral resolution. Herein, this reduction is avoided by a frequency-dependent <inline-formula> <tex-math notation="LaTeX">${F}$ </tex-math></inline-formula>-number. This <inline-formula> <tex-math notation="LaTeX">${F}$ </tex-math></inline-formula>-number derives from the far-field directivity pattern of a focused aperture and can be expressed in closed form. The <inline-formula> <tex-math notation="LaTeX">${F}$ </tex-math></inline-formula>-number, at low frequencies, widens the aperture to improve the lateral resolution. The <inline-formula> <tex-math notation="LaTeX">${F}$ </tex-math></inline-formula>-number, at high frequencies, narrows the aperture to avoid lobe overlaps and suppress grating lobes. Phantom and in vivo experiments with a Fourier-domain beamforming algorithm validated the proposed <inline-formula> <tex-math notation="LaTeX">${F}$ </tex-math></inline-formula>-number in CPWC. The lateral resolution, which was measured by the median lateral full-widths at half-maximum of wires, improved by up to 46.8% and 14.9% in a wire and a tissue phantom, respectively, in comparison to fixed <inline-formula> <tex-math notation="LaTeX">${F}$ </tex-math></inline-formula>-numbers. Grating lobe artifacts, which were measured by the median peak signal-to-noise ratios of wires, reduced by up to 9.9 dB in comparison to the full aperture. The proposed <inline-formula> <tex-math notation="LaTeX">${F}$ </tex-math></inline-formula>-number thus outperformed <inline-formula> <tex-math notation="LaTeX">${F}$ </tex-math></inline-formula>-numbers that were recently derived from the directivity of the array elements.
Evaluation of Male Breast Cancer and the Application of Sentinel Lymph Node Biopsy: A Multicenter Retrospective Study

Abstract Sentinel lymph node biopsy (SLNB) is currently used as a routine treatment for patients with breast cancer. However, it may not be applicable for patients with male breast cancer (MBC), because they have notably different clinicopathological features from those occurring in females. There is a lack of evidence of SLNB application and safe exemption from axillary lymph node dissection (ALND) in patients with MBC. This study aimed to evaluate the application of SLNB to provide information for the standardized treatment of patients with MBC. The MBC patient records from 4 institutions ranging from January 2001 to November 2020 were retrospectively reviewed. There were 220 patients with MBC with a median age of 60 (range 24-88) years and an average tumor size of 2.3 cm (range 0.5 cm-6.5 cm). Sixty-six percent of patients underwent SLNB, and 39% of them showed positive results. A total of 157 patients underwent ALND, while only half of them had positive nodes, causing unnecessary complications. For patients in the clinical early stage, we found that the SLNB showed a noninferiority to the ALND treatment in DFS (P = .18) and OS (P = .055). In conclusion, there are certain obstacles to the broad application of SLNB due to the lower proportion of patients with clinically negative lymph nodes. However, it is undeniable that SLNB can safely and effectively exempt patients with MBC at early stage with clinically negative nodes from ALND to reduce subsequent complications. It is still an ideal criterion for the axillary staging of patients with MBC.
Vertebral Body Sliding Osteotomy as a Surgical Strategy for the Treatment of Cervical Myelopathy: Complications and Pitfalls

Objective This retrospective cohort study has been aimed at evaluating the incidence of complications after vertebral body sliding osteotomy (VBSO) and analyzing some cases. Furthermore, the complications of VBSO were compared with those of anterior cervical corpectomy and fusion (ACCF). Methods This study included 154 patients who underwent VBSO (n = 109) or ACCF (n = 45) for cervical myelopathy and were followed up for > 2 years. Surgical complications, clinical and radiological outcomes were analyzed. Results The most common surgical complications after VBSO were dysphagia (n = 8, 7.3%) and significant subsidence (n = 6, 5.5%). There were 5 cases of C5 palsy (4.6%), followed by dysphonia (n = 4, 3.7%), implant failure (n = 3, 2.8%), pseudoarthrosis (n = 3, 2.8%), dural tears (n = 2, 1.8%), and reoperation (n = 2, 1.8%). C5 palsy and dysphagia did not require additional treatment and spontaneously resolved. The rates of reoperation (VBSO, 1.8%; ACCF, 11.1%; p = 0.02) and subsidence (VBSO, 5.5%; ACCF, 40%; p < 0.01) were significantly lower in VBSO than in ACCF. VBSO restored more C2–7 lordosis (VBSO, 13.9°±7.5°; ACCF, 10.1°±8.0°; p = 0.02) and segmental lordosis (VBSO, 15.7°±7.1°; ACCF, 6.6°±10.2°; p < 0.01) than ACCF. The clinical outcomes did not significantly differ between both groups. Conclusion VBSO has advantages over ACCF in terms of low rate of surgical complications related to reoperation and significant subsidence. However, dural tears may still occur despite the lessened need for ossified posterior longitudinal ligament lesion manipulation in VBSO; hence, caution is warranted.
A robustification of the two degree-of-freedom controller based upon multivariable generalized predictive control law and robust H∞ control for a doubly-fed induction generator

A robustification method of primary two degree-of-freedom (2-DOF) controllers is proposed in this paper to control the wind turbine system equipped with a doubly-fed induction generator DFIG. The proposed robustification method should follow the following three step-procedures. First, the primary 2-DOF controller is designed through the initial form of the multivariable generalized predictive control MGPC law to ensure a good tracking dynamic of reference trajectories. Second, the robust H ∞ controller is independently designed for the previous system to ensure good robustness properties of the closed-loop system against model uncertainties, neglecting dynamics and sensor noises. Finally, both above mentioned controllers are combined to design the robustified 2-DOF-MGPC controller using Youla parameterization method. Therefore, the obtained controller conserves the same good tracking dynamic that is provided by the primary 2-DOF-MGPC controller. It ensures the same good robustness properties which are produced by the robust H ∞ controller. A wind turbine system equipped with a DFIG is controlled by the robustified 2-DOF-MGPC controller. Its dynamic behaviour is modelled by an unstructured-output multiplicative uncertainty plant. The controller performances are valid by comparison with those given through both controllers, which are primary 2-DOF-MGPC and robust H ∞ controllers in time and frequency domains.
Injectivity of relational semantics for (connected) MELL proof-nets via Taylor expansion (extended abstract, cat. 1)

Starting from investigations on denotational semantics of System F (second order typed λ -calculus), in 1987 Girard [7] introduced linear logic (LL), a refinement of intuitionistic logic. He defines two new modalities, ! and ? , giving a logical status to structural rules and allowing to distinguish between linear resources (i.e. usable exactly once during the cut-elimination process) and resources available at will. One of the main features of LL is the possibility of representing proofs (and λ -terms) geometrically by means of particular graphs: proof-structures. Among proof-structures it is possible to characterize “in a geometric way” the ones corresponding to proofs in LL sequent calculus through the Danos-Regnier correctness criterion (see [2]): a proof-structure corresponds to a proof in LL sequent calculus if and only if it is a proof-net, i.e. it fulfills some conditions about acyclicity and connectedness. Ehrhard [3] introduced finiteness spaces, a denotational model of LL (and λ -calculus) which interprets formulas by topological vector spaces and proofs by analytical functions: in this model the operations of differentiation and Taylor expansion make sense. Ehrhard and Regnier [4, 5, 6] internalized these operations in the syntax and thus introduced differential linear logic DiLL (and differential λ -calculus), where the promotion rule (the only one in LL which is responsible for introducing the ! -modality and hence creating resources available at will) is replaced by three “finitary” rules which are perfectly symmetric to the rules for the ? -modality: this allows a more subtle analysis of the resources consumption during the cut-elimination process. At the syntactic level, Taylor expansion decomposes a LL proof-structure in a (infinite in general) formal sum of DiLL proof-structures (diffnets), each of which contains resources usable only a fixed number of times. Our contribution aims at looking further into the relationship between Taylor expansion and relational model (a well-known and simple denotational semantics of LL and λ -calculus). More precisely:
An electric field modeling study with meta-analysis to understand the antidepressant effects of transcranial direct current stimulation (tDCS)

Objective: Transcranial direct current stimulation (tDCS) has mixed effects for major depressive disorder (MDD) symptoms, partially owing to large inter-experimental variability in tDCS protocols and their correlated induced electric fields (E-fields). We investigated whether the E-field strength of distinct tDCS parameters was associated with antidepressant effect. Methods: A meta-analysis was performed with placebo-controlled clinical trials of tDCS enrolling MDD patients. PubMed, EMBASE, and Web of Science were searched from inception to March 10, 2023. Effect sizes of tDCS protocols were correlated with E-field simulations (SimNIBS) of brain regions of interest (bilateral dorsolateral prefrontal cortex [DLPFC] and bilateral subgenual anterior cingulate cortex [sgACC]). Moderators of tDCS responses were also investigated. Results: A total of 20 studies were included (21 datasets, 1,008 patients), using 11 distinct tDCS protocols. Results revealed a moderate effect for MDD (g = 0.41, 95%CI 0.18-0.64), while cathode position and treatment strategy were found to be moderators of response. A negative association between effect size and tDCS-induced E-field magnitude was seen, with stronger E-fields in the right frontal and medial parts of the DLPFC (targeted by the cathode) leading to smaller effects. No association was found for the left DLPFC and the bilateral sgACC. An optimized tDCS protocol is proposed. Conclusions: Our results highlight the need for a standardized tDCS protocol in MDD clinical trials. Registration number: PROSPERO CRD42022296246.
The Pregnant Smoker Stigma Scale - Self Stigma (P3S-SS): development and validation in pregnant smoking women in France

ABSTRACT Pregnancy smoking self-stigma may be associated with mental health and smoking cessation. This study aims to validate the Pregnant Smoker Stigma Scale – Self-Stigma (P3S-SS) assessing perceived and internalized stigma. Between May 2021 and May 2022, French pregnant smokers recruited online (n = 143) took the P3S-SS and other scales assessing depressive symptoms (EPDS), social inclusion (SIS), dissimulation, dependence (CDS-5), cessation self-efficacy (SEQ), and intention. The two versions of the scale include four dimensions: derogatory cognitions (“People think/I feel I am selfish”), negative emotions and behaviors (“People make me feel/smoking makes me feel guilty”), personal distress (“People/I feel sorry for me/myself”), and information provision (“People tell me/I think about the risks of smoking”). Confirmatory factor analyses and multiple regressions have been computed. Model fit was good for perceived stigma and internalized stigma (X2/df = 3.06, RMSEA = .124, AGFI = .982, SRMR = .068, CFI = .986, NNFI = .985; X2/df = 3.31, RMSEA = .14, AGFI = .977, SRMR = .087, CFI = .981, NNFI = .979). Controlling for dependence, cessation intention was positively predicted by perceived and internalized personal distress and negatively predicted by perceived negative emotions and behaviors (Adj R2 = .143, F(8,115) = 3.567, p = . 001). Controlling for dependence, dissimulation was positively predicted by internalized negative cognitions and perceived personal distress and negatively predicted by internalized personal distress (Adj R2 = .19, F(9,98) = 3.785, p = . 000). The P3S-SS opens up exciting avenues for further research. Stigma does not motivate women to stop smoking but increases distress and dissimulation.
Multiple Eschars in Scrub Typhus

Case: A 47-year-old male without any comorbidities was admitted with an intermittent fever of up to 102 (cid:1) F associated with chills and rigors and generalized weakness of 7 days duration. On examination, systolic blood pressure was 112mmHg, diastolic blood pressure was 68 mm Hg, pulse rate was 102 per minute, and respiratory rate was 18 per minute. Laboratory investigations showed hemoglobin of 9.9 g/dL, total leukocyte count of 12,600/mm 3 , and platelet count of 12,000/mm 3 , raised total bilirubin of 1.06mg/dL, alanine aminotransferase of 50U/L (2 – 41U/L), aspartate aminotransferase of 90U/L (2 – 40U/L), and raised international normalized ratio of 1.48. The possibility of tropical infection like scrub typhus, leptospirosis, and malaria were considered because the patient had presented in the post-monsoon season. Physical examination revealed two eschars: one on the left gluteal region (Figure 1A) and the other near the right popliteal region (Figure 1B). Serum IgM ELISA (InBios International, Inc.) was performed. The cutoff optical density (OD) of this kit according to the manufacturer ’ s instructions is 0.468, and the OD of this patient ’ s sample was . 4.0 (positive). Nested polymerase chain reaction for the partial 56kDa gene was determined for both eschars and was positive for Orientia tsutsugamushi (Figure 1C). 1 The positive amplicons were sent for the Sanger sequencing. The sequences were submitted to NCBI with following accession numbers