Miracle-dz/UniFAR-FTUs huggingface dataset:
An atlas of protein-protein interactions across mammalian tissues

Cellular processes arise from the dynamic organization of proteins in networks of physical interactions. Mapping the complete network of biologically relevant protein-protein interactions, the interactome, has therefore been a central objective of high-throughput biology. Yet, because widely used methods for high-throughput interaction discovery rely on heterologous expression or genetically manipulated cell lines, the dynamics of protein interactions across physiological contexts are poorly understood. Here, we use a quantitative proteomic approach combining protein correlation profiling with stable isotope labelling of mammals (PCP SILAM) to map the interactomes of seven mouse tissues. The resulting maps provide the first proteome-scale survey of interactome dynamics across mammalian tissues, revealing over 27,000 unique interactions with an accuracy comparable to the highest-quality human screens. We identify systematic suppression of cross-talk between the evolutionarily ancient housekeeping interactome and younger, tissue-specific modules. Rewiring of protein interactions across tissues is widespread, and is poorly predicted by gene expression or coexpression. Rewired proteins are tightly regulated by multiple cellular mechanisms and implicated in disease. Our study opens up new avenues to uncover regulatory mechanisms that shape in vivo interactome responses to physiological and pathophysiological stimuli in mammalian systems.
Muscleblind regulates Drosophila Dscam2 cell-type-specific alternative splicing

Alternative splicing of genes increases the number of distinct proteins in a cell. In the brain it is highly prevalent, presumably because proteome diversity is crucial for establishing the complex circuitry between trillions of neurons. To provide individual cells with different repertoires of protein isoforms, however, this process must be regulated. Previously, we found that the mutually exclusive alternative splicing of Drosophila Dscam2 exon 10A and 10B is tightly regulated and crucial for maintaining axon terminal size, dendritic morphology and synaptic numbers. Here, we show that Drosophila muscleblind (mbl), a conserved splicing factor implicated in myotonic dystrophy, controls Dscam2 alternative splicing. Removing mbl from cells that normally express isoform B induces the expression of isoform A and eliminates the expression of B, demonstrating that Mbl represses one alternative exon and selects the other. Consistent with these observations, we show that mbl expression is cell-type-specific and correlates with the expression of isoform B. Our study demonstrates how cell-type-specific expression of a splicing factor can provide neurons with unique protein isoforms.
L’analyse du chromosome Y

Malgre des difficultes initiales dans l’identification de polymorphismes genetiques de la partie non recombinante du chromosome Y humain, un grand nombre de marqueurs polymorphes sont aujourd’hui disponibles pour etablir des haplotypes ou haplogroupes caracteristiques d’individus ou de populations. Parmi ces marqueurs figurent les STR (Short Tandem Repeats) du chromosome Y, largement utilises au cours des dernieres annees pour etudier l’evolution de l’Homme et identifier des individus ou des filiations en medecine legale. Apres un bref rappel des particularites de ces marqueurs, nous presentons certaines des applications du typage genetique du chromosome Y.
A Novel Method Design Multiplexer Quaternary with CNTFET

Background and Objectives: In recent decades, due to the effect of the short channel, the use of CMOS transistors in the nanoscale has become a major concern. One option to deal with this issue is the use of nano-transistors. Methods: Using nano-transistors and multi-valued logic (MVL) can reduce the level of chips and connections and have a direct impact on power consumption. The present study reports the design of a new method of Multiplexers (MUXs) based on quaternary logic and transistors of carbon nanotubes (CNTFET) and having a new look at the layout and use of MUXs. Results:The use of special rotary functions and unary operators in Quaternary logic in the design of MUXs reduced the number of CNTFETs from 27% to 54%. Also, the use of MUXs in the Adder structure resulted in a 54% reduction in Power Delay Product (PDP) and a 17.5% to 85.6% reduction in CNTFET counts. Conclusion: The simulated results display a significant improvement in the fabrication of Adders, average power consumption, speed, and PDP compared to the current best-performing techniques in the literature. The proposed operators and circuits were evaluated under various operating conditions. The results show the stability of the proposed circuits.
Uber-Claws : unsupervised pattern classification for multi-unit extracellular neuronal burst extraction

UBER-CLAWS: UNSUPERVISED PATTERN CLASSIFICATION FOR MULTI-UNIT EXTRACELLULAR NEURONAL BURST EXTRACTION by Rama Natarajan To further an understanding of how a neuronal population generates patterns of rhythmic activity, the temporal dynamics of the group of neurons must be formalized. Essential to this pursuit, is the ability to reliably detect and separate the classes of single-unit neuronal activity from multi-unit extracellular signals recorded in a single channel. This study proposes a unified approach to automatically detect and classify single-unit bursts, and to observe the precise onset and offset of burst activity. Existing approaches to the problem fundamentally depend on the statistics of spike waveform variability, both extrinsic and intrinsic to the neuron. In contrast, the proposed approach depends on statistics that characterize the burst variability. An unsupervised learning procedure is implemented using hierarchical clustering to derive a complete and natural description of the variability in terms of clusters of bursts that possess strong internal similarities. Redundant solution vectors are used to parameterize each cluster, and a fuzzy classification approach assigns each burst to a class. Accuracy of the technique is demonstrated on in vivo and in vitro recordings of the triphasic pyloric rhythm in stomatogastric ganglion of crab Cancer borealis. The results, evaluated against a widely used manual classification approach, show that the technique performs detection and classification with comparable accuracy and quantifiable certainty, and is robust to background activity and noise. UBER-CLAWS: UNSUPERVISED PATTERN CLASSIFICATION FOR MULTI-UNIT EXTRACELLULAR NEURONAL BURST EXTRACTION
Long-Chain Acyl-CoA Synthetase 4–Mediated Fatty Acid Metabolism Sustains Androgen Receptor Pathway–Independent Prostate Cancer

Androgen deprivation therapy has led to elevated cases of androgen receptor (AR) pathway–independent prostate cancer with dysregulated fatty acid metabolism. However, it is unclear how prostate cancer cells sustain dysregulated fatty acid metabolism to drive AR-independent prostate cancer. Long-chain acyl-CoA synthetases (ACSL) catalyze the conversion of fatty acids into fatty acyl-CoAs that are required for fatty acid metabolism. In this study, we demonstrate that expression levels of ACSL3 and 4 were oppositely regulated by androgen–AR signaling in prostate cancer cells. AR served as a transcription suppressor to bind at the ACSL4 promoter region and inhibited its transcription. Inhibition of androgen–AR signaling significantly downregulated ACSL3 and PSA, but elevated ACSL4 levels. ACSL4 regulated a broad spectrum of fatty acyl-CoA levels, and its catalytic efficiency in fatty acyl-CoAs biosynthesis was about 1.9- to 4.3-fold higher than ACSL3. In addition, in contrast to ACSL3, ACSL4 significantly regulated global protein myristoylation or myristoylation of Src kinase in prostate cancer cells. Knockdown of ACSL4 inhibited the proliferation, migration, invasion, and xenograft growth of AR-independent prostate cancer cells. Our results suggest that the surge of ACSL4 levels by targeting AR signaling increases fatty acyl-CoAs biosynthesis and protein myristoylation, indicating the opposite, yet complementary or Yin-Yang regulation of ACSL3 and 4 levels in sustaining fatty acid metabolism when targeting androgen–AR signaling. This study reveals a mechanistic understanding of ACSL4 as a potential therapeutic target for treatment of AR-independent prostate cancer. Implications: AR coordinately regulates the expression of ACSL3 and ACSL4, such that AR pathway–independent prostate tumors become dependent on ACSL4-mediated fatty acid metabolism.
UMUCorpusClassifier: Compilation and evaluation of linguistic corpus for Natural Language Processing tasks

espanolLa construccion de un corpus anotado es una tarea que consume mucho tiempo. Aunque algunos investigadores han propuesto la anotacion automatica basada en heuristicas, estas no siempre son posibles. Ademas, incluso cuando la anotacion es realizada por personas puede haber discrepancias entre los mismos anotadores o de un anotador consigo mismo que influyen en la calidad del corpus. Por tanto, la falta de supervision sobre el proceso de anotacion puede llevar a corpus con baja calidad. En este trabajo, proponemos una demostracion de UMUCorpusClassifier, una herramienta PLN para ayudar a los investigadores a compilar corpus y tambien a coordinar y supervisar el proceso de anotacion. Esta herramienta facilita la monitorizacion diaria y permite detectar inconsistencias durante etapas tempranas del proceso de anotacion. EnglishThe development of an annotated corpus is a very time-consuming task. Although some researchers have proposed the automatic annotation of a corpus based on ad-hoc heuristics, valid hypotheses cannot always be made. Even when the annotation process is performed by human annotators, the quality of the corpus is heavily influenced by disagreements between annotators or with themselves. Therefore, the lack of supervision of the annotation process can lead to poor quality corpus. In this work, we propose a demonstration of UMUCorpusClassifier, a NLP tool for aid researches for compiling corpus as well as coordinating and supervising the annotation process. This tool eases the daily supervision process and permits to detect deviations and inconsistencies during early stages of the annotation process.
Is Transoral Surgery Still a Relevant Procedure in Atlantoaxial Instability?

ABSTRACT Background: The treatment of atlantoaxial instability (AAI) involves stable fixation and fusion with adequate decompression of spinal cord. After the advent of the Goel posterior joint manipulation technique, most of the once irreducible atlantoaxial dislocations (AAD) could be reduced and the need for transoral odontoidectomy became almost nil. Here we tried to iterate the indications of anterior transoral odontoid surgery for AAI in the current scenario. Methods: A retrospective study compiling the clinical, radiological, and surgical characteristics of 6 cases (5 scenarios). These patients underwent anterior transoral surgery alone or in combination with a posterior approach. Results: Two patients had a well-formed occipito-cervical fusion mass, with a displaced odontoid and unreduced C1-C2 joint causing cervical myelopathy. A middle-aged woman presented with unreduced AAD following failed C1-C2 joint distraction technique. A displaced dystopic os odontoideum ossicle was found in an adolescent boy, prohibiting the reduction of AAD. A young man had displacement of the fractured odontoid segment with intact transverse alar ligament and C1-C2 joint complex. One patient had a rare scenario of abnormal orientation of the C1-C2 joint. All 6 patients were successfully treated with adequate spinal cord decompression achieved by the anterior transoral route and stabilization by either the anterior approach itself or in combination with posterior surgery. All had significantly better postoperative outcomes except for 1 patient who expired due to poor respiratory reserve. Conclusion: We tried to emphasize the indications for using transoral anterior odontoid surgery over the posterior approach in the management of AAI. This will prevent the surgical technique of anterior odontoidectomy from becoming an obsolete procedure in the current practice.
Frailty, depression risk, and 10-year mortality in older adults: the FRADEA study

Abstract Objectives: To investigate if depression risk modifies the association between frailty and mortality in older adults. Design: Ongoing cohort study. Setting: Albacete city, Spain Participants: Eight hundred subjects, 58.8% women, over 70 years of age from the Frailty and Dependence in Albacete (FRADEA) study. Measurements: Frailty phenotype, Geriatric Depression Scale (GDS), comorbidity, disability, and drug use were collected at baseline. Six groups were categorized: (G1: non-frail/no depression risk; G2: non-frail/depression risk; G3: prefrail/no depression risk; G4: prefrail/depression risk; G5: frail/no depression risk; and G6: frail/depression risk). Mean follow-up was 2542 days (SD 1006). GDS was also analyzed as a continuous variable. The association between frailty and depression risk with 10-year mortality was analyzed. Results: Mean age was 78.5 years. Non-frail was 24.5%, prefrail 56.3%, frail 19.3%, and 33.5% at depression risk. Mean GDS score was 3.7 (SD 3.2), increasing with the number of frailty criteria (p < 0.001). Ten-year mortality rate was 44.9%. Mortality was 21.4% for the non-frail, 45.6% for the prefrail, and 72.7% for the frail participants, 56% for those with depression risk, and 39.3% for those without depression risk. Mean survival times for groups G1 to G6 were, respectively, 3390, 3437, 2897, 2554, 1887, and 1931 days. Adjusted mortality risk was higher for groups G3 (HR 2.1; 95% confidence interval (CI) 1.4–3.1), G4 (HR 2.5; 95% CI 1.7–3.8), G5 (HR 3.8; 95% CI 2.4–6.1), and G6 (HR 4.0; 95% CI 2.6–6.2), compared with G1 (p < 0.001). Interaction was found between frailty and depression risk, although they were independently associated with mortality. Conclusions: Depression risk increases mortality risk in prefrail older adults but not in non-frail and frail ones. Depression should be monitored in these older adults to optimize health outcomes. Factors modulating the relationship between frailty and depression should be explored in future studies.
Germination des graines produites par les plantes de deux lignées d' Oldenlandia corymbosa L. (Rubiacées) cultivées dans des conditions contrôlées

Les plantes de la lignée non dormante ne produisent toujours que des graines non dormantes. Par contre, les plantes de la lignée dormante donnent naissance à des fruits dont le pourcentage de graines dormantes est très variable. Dans cette lignée, c’est essentiellement l’âge de la plante au moment de la formation des fruits qui, détermine l’aptitude à la germination des graines qu’ils renferment. En particulier, la jeune plante produit beaucoup moins de graines dormantes que la plante âgée.
Local Delivery of Stromal Cell-Derived Factor-1α Improves the Pregnancy Rate of Injured Uterus through the Promotion of Endometrial and Vascular Regeneration

Severe infection and mechanical injury of the uterus may lead to infertility and miscarriage. Currently, there is a lack of effective treatment modality for functional repair of uterine injury. To address this clinical challenge, this study aimed to develop a chemotactic composite scaffold by incorporating recombinant human stromal cell-derived factor-1α (rhSDF-1α) into a silk fibroin-bacterial cellulose (SF-BC) membrane carrier. A rat model of uterine injury was utilized for this study, which was composed of three groups: blank control, implantation with SF-BC only or SF-BC loaded with rhSDF-1α. The tissue regeneration efficacy of the three groups were analyzed and compared. The results showed that SF-BC loaded with rhSDF-1α significantly enhanced endometrial regeneration and arteriogenesis of the injured rat uterus, which led to improved pregnancy outcomes, thus indicating much promise for functional uterine repair and regeneration.
Kernel Based Extreme Learning Machine in Identifying Dermatological Disorders

Extreme Learning Machine (ELM)has gained importance among various learning algorithms particularly related to multi classification problems. In this paper, kernel-based ELM is used to identify common skin disorders such as Bacterial Infection, Fungal Infection, Eczema and Scabies. A proper diagnosis of these diseases at primary stage is very essential to prevent future complications. The various kernel functions like Radial Basis Function, Polynomial kernel, Exponential Chi-Square kernel with ELM are applied on the skin dataset. In our study we measure accuracy and leaning time obtained using these kernels with ELM and Support Vector Machine (SVM). We also analyze our dataset on Conventional Single Layer feed Forward Network (SLFN). A comparative study of accuracy and learning time of all these learning algorithms is made and it is observed that ELM gives optimum learning time with good classification accuracy using exponential chi-square kernel.
Dermal mesenchymal stem cells promoted adhesion and migration of endothelial cells by integrin in psoriasis

The unusual dilatation of dermal capillaries and angiogenesis played important roles in psoriasis. Some genes and proteins of dermal mesenchymal stem cells (DMSCs) from psoriasis are abnormal and related to the function of endothelial cells (ECs). The present study was aimed to evaluate whether psoriatic DMSCs could affect adhesion and migration of ECs through neovascularization‐related integrins in psoriasis. Human DMSCs, collected from psoriasis lesions and healthy skin, respectively, were cocultured with human umbilical vein endothelial cells (HUVECs). The expression levels of three integrins, that is, αvβ3, αvβ5, and α5β1 in HUVECs were tested by quantitative real‐time polymerase chain reaction and Western blot analysis. The adhesion and migration of HUVECs were detected by adhesion assay and migration assay. The results showed that in psoriasis group, the expression of αVβ3 and α5β1 of HUVECs markedly increased 2.50‐ and 3.71‐fold in messenger RNA levels, and significantly increased 1.63‐ and 1.92‐fold in protein levels, comparing to healthy control group (all p < .05). But β5 was not significantly different between the two groups (p > .05). In addition, compared with control, psoriatic DMSCs promoted HUVECs adhesion by 1.62‐fold and migration by 2.91‐fold (all p < .05). In conclusion, psoriatic DMSCs impact HUVECs adhesion and migration by upregulating the expression of integrins αVβ3 and α5β1.
GIP receptor suppresses PAC1receptor‐mediated neuronal differentiation via formation of a receptor heterocomplex

Pituitary adenylate cyclase‐activating peptide (PACAP) receptor (PAC1R) is a class B Gprotein‐coupled receptor (GPCR) that is widely expressed in the human body and is involved in neuronal differentiation. As class B GPCRs are known to form heterocomplexes with family members, we hypothesized that PAC1R mediates neuronal differentiation through interaction with a class B GPCR. We used the BRET assay to identify potential interactions between PAC1R and 11 class B GPCRs. Gastric inhibitory polypeptide receptor (GIPR) and secretin receptor were identified as putative binding partners of PAC1R. The effect of heterocomplex formation by PAC1R on receptor activation was evaluated with the cyclic (c)AMP, luciferase reporter, and calcium signaling assays; and the effects on receptor internalization and subcellular localization were examined by confocal microscopy. The results suggested he PAC1R/GIPR heterocomplex suppressed signaling events downstream of PAC1R, including cAMP production, serum response element and calcium signaling, and β‐arrestin recruitment. Protein–protein interaction was analyzed in silico, and induction of neuronal differentiation by the PAC1R heterocomplex was assessed in SH‐SY5Y neuronal cells by measure the morphological changes and marker genes expression by real‐time quantitative PCR and western blot. Over‐expression of GIPR suppressed PACAP/PAC1R‐mediated neuronal differentiation and the differentiation markers expression in SH‐SY5Y cells. GIPR regulates neuronal differentiation through heterocomplex formation with PAC1R.
Surgery without Scars: Right Lateral Access for Minimally Invasive Aortic Valve Replacement

Abstract As part of an institutionally driven holistic concept, named the “360-degree approach,” all established surgical access routes —full sternotomy, partial upper sternotomy, and right anterolateral thoracotomy using the second interspace—are supported. The surgical toolbox now is completed by adding a further approach: through a 5- to7-cm skin incision in the right anterior axillary line, the third interspace is used for a minimally invasive aortic valve surgery providing striking exposition of the aortic valve and resulting in superior cosmetics with nearly no visible scars. The choice for the one or other method is institutionally driven and based on risk profiles, as well as anatomical and physiognomic considerations.
Living with Family Is Directly Associated with Regular Dental Checkup and Indirectly Associated with Gingival Status among Japanese University Students: A 3-Year Cohort Study

Although some studies showed that lifestyle was associated with oral health behavior, few studies investigated the association between household type and oral health behavior. The aim of this prospective cohort study was to investigate the association between household type, oral health behavior, and periodontal status among Japanese university students. Data were obtained from 377 students who received oral examinations and self-questionnaires in 2016 and 2019. We assessed periodontal status using the percentage of bleeding on probing (%BOP), probing pocket depth, oral hygiene status, oral health behaviors, and related factors. We used structural equation modeling to determine the association between household type, oral health behaviors, gingivitis, and periodontitis. At follow-up, 252 students did not live with their families. The mean ± standard deviation of %BOP was 35.5 ± 24.7 at baseline and 32.1 ± 25.3 at follow-up. In the final model, students living with their families were significantly more likely to receive regular dental checkup than those living alone. Regular checkup affected the decrease in calculus. The decrease in calculus affected the decrease in %BOP over 3 years. Living with family was directly associated with regular dental checkups and indirectly contributed to gingival status among Japanese university students.
Functional characteristic and differential expression of myostatin in Chlamys nobilis

ABSTRACT Myostatin (MSTN) was a conserved negative regulatory protein of muscle growth and development in numerous species. In this study, the MSTN gene was cloned and characterized from a noble scallop, Chlamys nobilis, and it was named CN-MSTN. To investigate the molecular characterization of MSTN and its gene expression profile of spatio-temporal, we isolated the MSTN cDNA sequence in C. nobilis and analysed expression patterns using quantitative real-time PCR. CN-MSTN cDNA contained a 1,374 bp open reading frame that encoded a 458 amino acids. Furthermore, the result of 3D model indicated that CN-MSTN mature peptide was similar to that of Chlamys farreri. Additionally, based on both the nucleotide and amino acid datasets, phylogenetic trees indicated that C. nobilis has the highest similarity with homologues of C. farreri. The expression patterns of different stages showed that MSTN expression was markedly higher in the gastrulae period. Additionally, remarkable expression of MSTN was observed in adductor muscle than with other tissues. Our data would provide expression and phylogenetic information of this economical important sea food, noble scallop.