Miracle-dz/UniFAR-FTUs huggingface dataset:
Photoreceptor disc incisures form as an adaptive mechanism ensuring the completion of disc enclosure

The first steps of vision take place within a stack of tightly packed disc-shaped membranes, or ‘discs’, located in the outer segment compartment of photoreceptor cells. In rod photoreceptors, discs are enclosed inside the outer segment and contain deep indentations in their rims called ‘incisures’. The presence of incisures has been documented in a variety of species, yet their role remains elusive. In this study, we combined traditional electron microscopy with three-dimensional electron tomography to demonstrate that incisures are formed only after discs become completely enclosed. We also observed that, at the earliest stage of their formation, discs are not round as typically depicted but rather are highly irregular in shape and resemble expanding lamellipodia. Using genetically manipulated mice and frogs and measuring outer segment protein abundances by quantitative mass spectrometry, we further found that incisure size is determined by the molar ratio between peripherin-2, a disc rim protein critical for the process of disc enclosure, and rhodopsin, the major structural component of disc membranes. While a high perpherin-2 to rhodopsin ratio causes an increase in incisure size and structural complexity, a low ratio precludes incisure formation. Based on these data, we propose a model whereby normal rods express a modest excess of peripherin-2 over the amount required for complete disc enclosure in order to ensure that this important step of disc formation is accomplished. Once the disc is enclosed, the excess peripherin-2 incorporates into the rim to form an incisure.
Adenine nucleotide carrier protein dysfunction in human disease

Adenine nucleotide translocase (ANT) is the prototypical member of the mitochondrial carrier protein family, primarily involved in ADP/ATP exchange across the inner mitochondrial membrane. Several carrier proteins evolutionarily related to ANT, including SLC25A24 and SLC25A25, are believed to promote the exchange of cytosolic ATP‐Mg2+ with phosphate in the mitochondrial matrix. They allow a net accumulation of adenine nucleotides inside mitochondria, which is essential for mitochondrial biogenesis and cell growth. In the last two decades, mutations in the heart/muscle isoform 1 of ANT (ANT1) and the ATP‐Mg2+ transporters have been found to cause a wide spectrum of human diseases by a recessive or dominant mechanism. Although loss‐of‐function recessive mutations cause a defect in oxidative phosphorylation and an increase in oxidative stress which drives the pathology, it is unclear how the dominant missense mutations in these proteins cause human diseases. In this review, we focus on how yeast was productively used as a model system for the understanding of these dominant diseases. We also describe the relationship between the structure and function of ANT and how this may relate to various pathologies. Particularly, mutations in Aac2, the yeast homolog of ANT, were recently found to clog the mitochondrial protein import pathway. This leads to mitochondrial precursor overaccumulation stress (mPOS), characterized by the toxic accumulation of unimported mitochondrial proteins in the cytosol. We anticipate that in coming years, yeast will continue to serve as a useful model system for the mechanistic understanding of mitochondrial protein import clogging and related pathologies in humans.
Cytological spectrum of testicular malignancies with histopathological correlation: A retrospective analysis

Testicular malignancy is the most common solid organ cancer occurring in young men. The most common testicular malignancy is germ cell tumor. Extragonadal malignancies such as lymphomas are rare. Testicular fine‐needle aspiration cytology (FNAC) in cancer is a bit controversial amidst fear of tumor seeding along the needle tract. Nevertheless, its largely safe, cost‐effective technique providing a quick and fairly reliable diagnosis.
A Surgical Desirability of Outcome Ranking (DOOR) Reveals Complex Relationships Between Race/Ethnicity, Insurance Type, and Neighborhood Deprivation

Objective: Develop an ordinal Desirability of Outcome Ranking (DOOR) for surgical outcomes to examine complex associations of Social Determinants of Health. Background: Studies focused on single or binary composite outcomes may not detect health disparities. Methods: Three health care system cohort study using NSQIP (2013–2019) linked with EHR and risk-adjusted for frailty, preoperative acute serious conditions (PASC), case status and operative stress assessing associations of multilevel Social Determinants of Health of race/ethnicity, insurance type (Private 13,957; Medicare 15,198; Medicaid 2835; Uninsured 2963) and Area Deprivation Index (ADI) on DOOR and the binary Textbook Outcomes (TO). Results: Patients living in highly deprived neighborhoods (ADI>85) had higher odds of PASC [adjusted odds ratio (aOR)=1.13, CI=1.02–1.25, P<0.001] and urgent/emergent cases (aOR=1.23, CI=1.16–1.31, P<0.001). Increased odds of higher/less desirable DOOR scores were associated with patients identifying as Black versus White and on Medicare, Medicaid or Uninsured versus Private insurance. Patients with ADI>85 had lower odds of TO (aOR=0.91, CI=0.85–0.97, P=0.006) until adjusting for insurance. In contrast, patients with ADI>85 had increased odds of higher DOOR (aOR=1.07, CI=1.01–1.14, P<0.021) after adjusting for insurance but similar odds after adjusting for PASC and urgent/emergent cases. Conclusions: DOOR revealed complex interactions between race/ethnicity, insurance type and neighborhood deprivation. ADI>85 was associated with higher odds of worse DOOR outcomes while TO failed to capture the effect of ADI. Our results suggest that presentation acuity is a critical determinant of worse outcomes in patients in highly deprived neighborhoods and without insurance. Including risk adjustment for living in deprived neighborhoods and urgent/emergent surgeries could improve the accuracy of quality metrics.
Aggressive local therapy for de novo metastatic breast cancer: Challenges and updates (Review)

Systemic therapy has been viewed as the mainstay for de novo metastatic breast cancer (dnMBC). However, as dnMBC is highly heterogeneous both biologically and clinically, and with ever-improving systemic strategies, it has been implied that the local therapy of the primary tumor (PT) may be beneficial for certain patients with dnMBC. However, the results from retrospective studies have been questioned due to their selection bias and retrospective nature. To the best of our knowledge, there are two published randomized clinical trials addressing this issue with conflicting conclusions: i) TATA study from India indicated no overall survival (OS) superiority with early local radiotherapy (LRT); and ii) MF07-01 indicated a 5-year OS rate improvement of 17% with upfront LRT. The updated results of a randomized phase III ECOG-ACRIN E2108 trial released in the 2020 American Society of Clinical Oncology (ASCO) meeting reported a negative survival effect of early LRT treatment in patients with dnMBC responding to initial systemic treatment, despite LRT significantly reducing the locoregional failure. Thus, a number of issues, such as the exact value of LRT, the optimal means of LRT (surgery and/or RT to the PT), the ideal timing of LRT and the population most likely to benefit from LRT, warrant further investigation. Herein, the related studies focusing on these aspects were comprehensively reviewed and a decision algorithm was proposed to select suitable patients with dnMBC for reasonable LRT. Generally, upfront systemic therapy is recommended. For good respondents and a subgroup of favorable profiles (young age, good general condition, low tumor burden, hormone receptor-positive and so on), radical LRT including PT surgery followed by RT and the resection of distant metastases is recommended. LRT should also be administered if the PT is still symptomatic. LRT may benefit patients with dnMBC due to the following reasons: Control of the PT decreases tumor burden, eliminates the source of dissemination, enhances the sensitivity to therapy and exerts positive immunomodulation. Therefore, the treatment paradigm for dnMBC may change from ‘palliative LRT’ into ‘curative LRT’ in a highly selected entity with careful evaluation.
Statistical mechanics approaches to optimization and inference

Nowadays, typical methodologies employed in statistical physics are successfully applied to a huge set of problems arising from different research fields. In this thesis I will propose several statistical mechanics based models able to deal with two types of problems: optimization and inference problems. The intrinsic difficulty that characterizes both problems is that, due to the hard combinatorial nature of optimization and inference, finding exact solutions would require hard and impractical computations. In fact, the time needed to perform these calculations, in almost all cases, scales exponentially with respect to relevant parameters of the system and thus cannot be accomplished in practice. As combinatorial optimization addresses the problem of finding a fair configuration of variables able to minimize/maximize an objective function, inference seeks a posteriori the most fair assignment of a set of variables given a partial knowledge of the system. These two problems can be re-phrased in a statistical mechanics framework where elementary components of a physical system interact according to the constraints of the original problem. The information at our disposal can be encoded in the Boltzmann distribution of the new variables which, if properly investigated, can provide the solutions to the original problems. As a consequence, the methodologies originally adopted in statistical mechanics to study and, eventually, approximate the Boltzmann distribution can be fruitfully applied for solving inference and optimization problems. The structure of the thesis follows the path covered during the three years of my Ph.D. At first, I will propose a set of combinatorial optimization problems on graphs, the Prize collecting and the Packing of Steiner trees problems. The tools used to face these hard problems rely on the zero-temperature implementation of the Belief Propagation algorithm, called Max Sum algorithm. The second set of problems proposed in this thesis falls under the name of linear estimation problems. One of them, the compressed sensing problem, will guide us in the modelling of these problems within a Bayesian framework along with the introduction of a powerful algorithm known as Expectation Propagation or Expectation Consistent in statistical physics. I will propose a similar approach to other challenging problems: the inference of metabolic fluxes, the inverse problem of the electro-encephalography and the reconstruction of tomographic images.
Targeting Solid Cancers with a Cancer-Specific Monoclonal Antibody to Surface Expressed Aberrantly O-glycosylated Proteins

Abstract The lack of antibodies with sufficient cancer selectivity is currently limiting the treatment of solid tumors by immunotherapies. Most current immunotherapeutic targets are tumor-associated antigens that are also found in healthy tissues and often do not display sufficient cancer selectivity to be used as targets for potent antibody-based immunotherapeutic treatments, such as chimeric antigen receptor (CAR) T cells. Many solid tumors, however, display aberrant glycosylation that results in expression of tumor-associated carbohydrate antigens that are distinct from healthy tissues. Targeting aberrantly glycosylated glycopeptide epitopes within existing or novel glycoprotein targets may provide the cancer selectivity needed for immunotherapy of solid tumors. However, to date only a few such glycopeptide epitopes have been targeted. Here, we used O-glycoproteomics data from multiple cell lines to identify a glycopeptide epitope in CD44v6, a cancer-associated CD44 isoform, and developed a cancer-specific mAb, 4C8, through a glycopeptide immunization strategy. 4C8 selectively binds to Tn-glycosylated CD44v6 in a site-specific manner with low nanomolar affinity. 4C8 was shown to be highly cancer specific by IHC of sections from multiple healthy and cancerous tissues. 4C8 CAR T cells demonstrated target-specific cytotoxicity in vitro and significant tumor regression and increased survival in vivo. Importantly, 4C8 CAR T cells were able to selectively kill target cells in a mixed organotypic skin cancer model having abundant CD44v6 expression without affecting healthy keratinocytes, indicating tolerability and safety.
ENIGMA CHEK2gether Project: A Comprehensive Study Identifies Functionally Impaired CHEK2 Germline Missense Variants Associated with Increased Breast Cancer Risk

Abstract Purpose: Germline pathogenic variants in CHEK2 confer moderately elevated breast cancer risk (odds ratio, OR ∼ 2.5), qualifying carriers for enhanced breast cancer screening. Besides pathogenic variants, dozens of missense CHEK2 variants of uncertain significance (VUS) have been identified, hampering the clinical utility of germline genetic testing (GGT). Experimental Design: We collected 460 CHEK2 missense VUS identified by the ENIGMA consortium in 15 countries. Their functional characterization was performed using CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1–CHEK2-knockout cells. Concordant results in both functional assays were used to categorize CHEK2 VUS from 12 ENIGMA case–control datasets, including 73,048 female patients with breast cancer and 88,658 ethnicity-matched controls. Results: A total of 430/460 VUS were successfully analyzed, of which 340 (79.1%) were concordant in both functional assays and categorized as functionally impaired (N = 102), functionally intermediate (N = 12), or functionally wild-type (WT)–like (N = 226). We then examined their association with breast cancer risk in the case–control analysis. The OR and 95% CI (confidence intervals) for carriers of functionally impaired, intermediate, and WT-like variants were 2.83 (95% CI, 2.35–3.41), 1.57 (95% CI, 1.41–1.75), and 1.19 (95% CI, 1.08–1.31), respectively. The meta-analysis of population-specific datasets showed similar results. Conclusions: We determined the functional consequences for the majority of CHEK2 missense VUS found in patients with breast cancer (3,660/4,436; 82.5%). Carriers of functionally impaired missense variants accounted for 0.5% of patients with breast cancer and were associated with a moderate risk similar to that of truncating CHEK2 variants. In contrast, 2.2% of all patients with breast cancer carried functionally wild-type/intermediate missense variants with no clinically relevant breast cancer risk in heterozygous carriers.
A perspective on cross‐kingdom RNA interference in mutualistic symbioses

Summary RNA interference (RNAi) is arguably one of the more versatile mechanisms in cell biology, facilitating the fine regulation of gene expression and protection against mobile genomic elements, whilst also constituting a key aspect of induced plant immunity. More recently, the use of this mechanism to regulate gene expression in heterospecific partners – cross‐kingdom RNAi (ckRNAi) – has been shown to form a critical part of bidirectional interactions between hosts and endosymbionts, regulating the interplay between microbial infection mechanisms and host immunity. Here, we review the current understanding of ckRNAi as it relates to interactions between plants and their pathogenic and mutualistic endosymbionts, with particular emphasis on evidence in support of ckRNAi in the arbuscular mycorrhizal symbiosis.
Predicting lifespan-extending chemical compounds for C. elegans with machine learning and biologically interpretable features

Recently, there has been a growing interest in the development of pharmacological interventions targeting ageing, as well as in the use of machine learning for analysing ageing-related data. In this work, we use machine learning methods to analyse data from DrugAge, a database of chemical compounds (including drugs) modulating lifespan in model organisms. To this end, we created four types of datasets for predicting whether or not a compound extends the lifespan of C. elegans (the most frequent model organism in DrugAge), using four different types of predictive biological features, based on: compound-protein interactions, interactions between compounds and proteins encoded by ageing-related genes, and two types of terms annotated for proteins targeted by the compounds, namely Gene Ontology (GO) terms and physiology terms from the WormBase’s Phenotype Ontology. To analyse these datasets, we used a combination of feature selection methods in a data pre-processing phase and the well-established random forest algorithm for learning predictive models from the selected features. In addition, we interpreted the most important features in the two best models in light of the biology of ageing. One noteworthy feature was the GO term “Glutathione metabolic process”, which plays an important role in cellular redox homeostasis and detoxification. We also predicted the most promising novel compounds for extending lifespan from a list of previously unlabelled compounds. These include nitroprusside, which is used as an antihypertensive medication. Overall, our work opens avenues for future work in employing machine learning to predict novel life-extending compounds.
Prevalence of Immunomodulator Use as Combination Therapy With Vedolizumab or Ustekinumab in Inflammatory Bowel Disease

INTRODUCTION: The benefit of adding an immunomodulator to vedolizumab and ustekinumab remains unclear and may compromise the safety of these biologics. We evaluated the prevalence and predictors of immunomodulator use with vedolizumab or ustekinumab in patients with inflammatory bowel disease in a large longitudinal cohort. METHODS: Clinical information was ascertained from electronic medical records of patients enrolled in TARGET-IBD, a prospective longitudinal observational cohort of patients with inflammatory bowel disease (IBD) at 34 sites. The prevalence of immunomodulator use with vedolizumab, ustekinumab, and antitumor necrosis factor therapies and predictors of immunomodulator use with vedolizumab and ustekinumab were estimated. Rates of combination therapy were additionally stratified by time from drug approval. RESULTS: Four thousand thirty-nine adults with IBD were identified, of whom 18.8% were treated with vedolizumab and 13.0% were treated with ustekinumab. Combination therapy with vedolizumab and ustekinumab exceeded 30% (30.7% and 36.2%, respectively) and was more likely in those with perianal disease or previous biologic exposure. Age and presence of extraintestinal manifestations did not consistently predict the use of an immunomodulator. Combination therapy decreased in the years after drug approval. DISCUSSION: Combination therapy with vedolizumab or ustekinumab was common and was associated with perianal disease and greater exposure to other biologics, although the practice is decreasing with time. Further data are needed to determine the efficacy and safety of combination therapy in patients initiating vedolizumab or ustekinumab for IBD.
Vitamin D deficiency contributes to overtraining syndrome in excessive trained C57BL/6 mice

Overtraining syndrome is a condition resulting from excessive training load associated with inadequate recovery and poor sleep quality, leading to performance decrements and fatigue. Here we hypothesized that vitamin D (VitD) deficiency is a lead factor in the development of the overtraining syndrome. To test this hypothesis, two groups of 60‐week‐old C57BL/6 mice followed a 16‐week excessive eccentric‐based overtraining by excessive downhill running with or without dietary VitD depletion (EX and EX‐D− groups). Two control groups were trained by uphill running at the same load with or without VitD depletion (CX and CX‐D− groups). Handgrip strength decreased throughout the protocol for all groups but the decrease was sharper in EX‐D− group (VitD × training, p = 0.0427). At the end of the protocol, the mass of Triceps brachii muscle, which is heavily stressed by eccentric contractions, was reduced in eccentric‐trained groups (training effect, p = 0.0107). This atrophy was associated with a lower concentration of the anabolic myokine IL‐15 (training effect, p = 0.0314) and a tendency to a higher expression of the atrogene cathepsin‐L (training effect, p = 0.0628). VitD depletion led to a 50% decrease of the fractional protein synthesis rate in this muscle (VitD effect, p = 0.0004) as well as decreased FGF21 (VitD effect, p = 0.0351) and increased osteocrin (VitD effect, p = 0.038) concentrations that would lead to metabolic defects. Moreover, the proportion of anti‐inflammatory Th2 lymphocytes was significantly decreased by the combination of eccentric training with VitD depletion (vitD × training, p = 0.0249) suggesting a systemic inflammation. Finally, exploratory behavior time of mice was decreased by VitD depletion (VitD effect, p = 0.0146) suggesting a cognitive dysfunction. Our results suggest that VitD deficiency exacerbates the effects of overtraining.
Sublingual floor of Rahmani sheep (Ovis aries): A scanning electron microscopy and histomorphology analysis

The current study investigated the sublingual floor of Rahmani sheep (Ovis aries). Samples from nine healthy adult sheep have been analysed using morphometrical, scanning electron microscopic (SEM), and histological examination. The sublingual floor of the sheep was formed of a rostral prefrenular part (spatula‐shaped) and two lateral sublingual recesses. Right and left sublingual caruncles were asymmetrical in length and each one had a serrated border, divided into three papillae. At higher magnifications, the three papillae of the sublingual caruncle's edge were variable in shape, with other two papillae were demonstrated underneath the caruncle. Each sublingual recess had a sublingual fold (plica sublingualis) extended from the level of frenulum linguae till the glossopalatine arch, bordered with caudolaterally directed papillae till the level of first lower molar cheek teeth. The sublingual salivary glands were mixed (seromucoid) type. The glandular lobule consisted of mucous acini and sporadic serous acini, as well as the presence of some mucous acini capped by acidophilic cells, serous demilunes. The mucous acinus was formed of pyramidal mucous cells with pale stained cytoplasm and basally located nuclei. Two ducts; major sublingual and submandibular ducts were observed within the submucosa of the sublingual caruncle. The sublingual ductal pseudostratified columnar epithelium was interspersed by more goblet cells than that of the submandibular duct. Collagen fibres around the glandular lobules, intralobular and interlobular excretory ducts as well as the connective core of the papillae were noticed. By SEM, two epithelium‐lined pits on the surface of the sublingual floor mucosa caudal to the central incisive teeth were termed orobasal organ. As the first study to give a comprehensive analysis of the sheeps' sublingual floor, this one serves as a baseline for future clinical studies.