Explainable machine learning models for early gastric cancer diagnosis.

Gastric cancer remains a significant global health concern, with a notably high incidence in East Asia. This paper explores the potential of explainable machine learning models in enhancing the early diagnosis of gastric cancer. Through comprehensive evaluations, various machine learning models, including WeightedEnsemble, CatBoost, and RandomForest, demonstrated high potential in accurately diagnosing early gastric cancer. The study emphasizes the importance of model explainability in medical diagnostics, showing how transparent, explainable models can increase trust and clinical acceptance, thereby improving diagnostic accuracy and patient outcomes. This research not only highlights key biomarkers and clinical features critical for early detection but also presents a versatile approach that could be applied to other medical diagnostics, promoting broader adoption of machine learning in clinical settings.

Hair follicle-resident progenitor cells are a major cellular contributor to heterotopic subcutaneous ossifications in a mouse model of Albright hereditary osteodystrophy.

Heterotopic ossifications (HOs) are the pathologic process by which bone inappropriately forms outside of the skeletal system. Despite HOs being a persistent clinical problem in the general population, there are no definitive strategies for their prevention and treatment due to a limited understanding of the cellular and molecular mechanisms contributing to lesion development. One disease in which the development of heterotopic subcutaneous ossifications (SCOs) leads to morbidity is Albright hereditary osteodystrophy (AHO). AHO is caused by heterozygous inactivation of GNAS, the gene that encodes the α-stimulatory subunit (Gαs) of G proteins. Previously, we had shown using our laboratory's AHO mouse model that SCOs develop around hair follicles (HFs). Here we show that SCO formation occurs due to inappropriate expansion and differentiation of HF-resident stem cells into osteoblasts. We also show in AHO patients and mice that Secreted Frizzled Related Protein 2 (SFRP2) expression is upregulated in regions of SCO formation and that elimination of Sfrp2 in male AHO mice exacerbates SCO development. These studies provide key insights into the cellular and molecular mechanisms contributing to SCO development and have implications for potential therapeutic modalities not only for AHO patients but also for patients suffering from HOs with other etiologies.

Prevalence of Chiari malformation type 1 is increased in pseudohypoparathyroidism type 1A and associated with aberrant bone development.

BACKGROUND: Albright hereditary osteodystrophy (AHO) is caused by heterozygous inactivating mutations in GNAS. Patients with maternally-inherited mutations develop pseudohypoparathyroidism type 1A (PHP1A) with multi-hormone resistance and aberrant craniofacial and skeletal development among other abnormalities. Chiari malformation type 1 (CM1), a condition in which brain tissue extends into the spinal canal when the skull is too small, has been reported in isolated cases of PHP1A. It has been hypothesized to be associated with growth hormone (GH) deficiency. Given the adverse clinical sequelae that can occur if CM1 goes unrecognized, we investigated the previously undetermined prevalence of CM1, as well as any potential correlations with GH status, given the known increased prevalence of GH deficiency in PHP1A. We also investigated these metrics for low lying cerebellar tonsils (LLCT), defined as tonsillar descent less than 5 mm below the foramen magnum. In addition, we investigated possible correlations of CM1/LLCT with advanced hand/wrist bone ages and craniofacial abnormalities known to occur in PHP1A to determine whether premature chondrocyte differentiation and/or aberrant craniofacial development could be potential etiologies of CM1/LLCT through both human studies and investigations of our AHO mouse model. METHODS: We examined patients with PHP1A in our clinic and noticed CM1 more frequently than expected. Therefore, we set out to determine the true prevalence of CM1 and LLCT in a cohort of 54 mutation-confirmed PHP1A participants who had clinically-indicated brain imaging. We examined potential correlations with GH status, clinical features, biological sex, genotype, and hand/wrist bone age determinations. In addition, we investigated the craniofacial development in our mouse model of AHO (Gnas E1+/-m) by histologic analyses, dynamic histomorphometry, and micro-computerized tomographic imaging (MCT) in order to determine potential etiologies of CM1/LLCT in PHP1A. RESULTS: In our cohort of PHP1A, the prevalence of CM1 is 10.8%, which is at least 10-fold higher than in the general population. If LLCT is included, the prevalence increases to 21.7%. We found no correlation with GH status, biological sex, genotype, or hand/wrist bone age. Through investigations of our Gnas E1+/-m mice, the correlate to PHP1A, we identified a smaller cranial vault and increased cranial dome angle with evidence of hyperostosis due to increased osteogenesis. We also demonstrated that there was premature closure of the spheno-occipital synchondrosis (SOS), a cartilaginous structure essential to the development of the cranial base. These findings lead to craniofacial abnormalities and could contribute to CM1 and LLCT development in PHP1A. CONCLUSION: The prevalence of CM1 is at least 10-fold higher in PHP1A compared to the general population and 20-fold higher when including LLCT. This is independent of the GH deficiency that is found in approximately two-thirds of patients with PHP1A. In light of potential serious consequences of CM1, clinicians should have a low threshold for brain imaging. Investigations of our AHO mouse model revealed aberrant cranial formation including a smaller cranium, increased cranial dome angle, hyperostosis, and premature SOS closure rates, providing a potential etiology for the increased prevalence of CM1 and LLCT in PHP1A.

Parental Origin of Gsα Inactivation Differentially Affects Bone Remodeling in a Mouse Model of Albright Hereditary Osteodystrophy.

Albright hereditary osteodystrophy (AHO) is caused by heterozygous inactivation of GNAS, a complex locus that encodes the alpha-stimulatory subunit of heterotrimeric G proteins (Gsα) in addition to NESP55 and XLαs due to alternative first exons. AHO skeletal manifestations include brachydactyly, brachymetacarpia, compromised adult stature, and subcutaneous ossifications. AHO patients with maternally-inherited GNAS mutations develop pseudohypoparathyroidism type 1A (PHP1A) with resistance to multiple hormones that mediate their actions through G protein-coupled receptors (GPCRs) requiring Gsα (eg, parathyroid hormone [PTH], thyroid-stimulating hormone [TSH], growth hormone-releasing hormone [GHRH], calcitonin) and severe obesity. Paternally-inherited GNAS mutations cause pseudopseudohypoparathyroidism (PPHP), in which patients have AHO skeletal features but do not develop hormonal resistance or marked obesity. These differences between PHP1A and PPHP are caused by tissue-specific reduction of paternal Gsα expression. Previous reports in mice have shown loss of Gsα causes osteopenia due to impaired osteoblast number and function and suggest that AHO patients could display evidence of reduced bone mineral density (BMD). However, we previously demonstrated PHP1A patients display normal-increased BMD measurements without any correlation to body mass index or serum PTH. Due to these observed differences between PHP1A and PPHP, we utilized our laboratory's AHO mouse model to address whether Gsα heterozygous inactivation differentially affects bone remodeling based on the parental inheritance of the mutation. We identified fundamental distinctions in bone remodeling between mice with paternally-inherited (GnasE1+/-p) versus maternally-inherited (GnasE1+/-m) mutations, and these findings were observed predominantly in female mice. Specifically, GnasE1+/-p mice exhibited reduced bone parameters due to impaired bone formation and enhanced bone resorption. GnasE1+/-m mice, however, displayed enhanced bone parameters due to both increased osteoblast activity and normal bone resorption. These in vivo distinctions in bone remodeling between GnasE1+/-p and GnasE1+/-m mice could potentially be related to changes in the bone microenvironment driven by calcitonin-resistance within GnasE1+/-m osteoclasts. Further studies are warranted to assess how Gsα influences osteoblast-osteoclast coupling. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ1 RNA Riboswitches.

Single-stranded noncoding regulatory RNAs, as exemplified by bacterial riboswitches, are highly dynamic. The conformational dynamics allow the riboswitch to reach maximum switching efficiency under appropriate conditions. Here we characterize the conformational dynamics of preQ1 riboswitches from mesophilic and thermophilic bacterial species at various temperatures. With the integrative use of small-angle X-ray scattering, NMR, and molecular dynamics simulations, we model the ensemble-structures of the preQ1 riboswitch aptamers without or with a ligand bound. We show that the preQ1 riboswitch is sufficiently dynamic and fluctuating among multiple folding intermediates only near the physiological temperature of the microorganism. The hierarchical folding dynamics of the RNA involves the docking of 3'-tail to form a second RNA helix and the helical stacking to form an H-type pseudoknot structure. Further, we show that RNA secondary and tertiary dynamics can be modulated by temperature and by the length of an internal loop. The coupled equilibria between RNA folding intermediates are essential for preQ1 binding, and a four-state exchange model can account for the change of ligand-triggered switching efficiency with temperature. Together, we have established a relationship between the hierarchical dynamics and riboswitch function, and illustrated how the RNA adapts to high temperature.

Clinical Analysis of Magnetic Nanoparticle Contrast Agent in the Diagnosis of Occult Fracture by Multislice Spiral CT and MRI.

To investigate the differences in the diagnosis and treatment of occult fractures between multi-slice spiral CT (CT) and magnetic resonance imaging (MRI) using I/Fe3O4 nanometer contrast agent. This retrospective study analyzed the clinical data of 60 patients with occult fractures and compared the diagnosis results of multislice CT (observation group) and MRI (control group). All the contrast agents used were I/Fe3O4 nanometer contrast agents. In the control group, 55 cases (91.67%) were detected on T1-weighted imaging versus 58 cases (96.67) on T2-weighted imaging. In the observation group, 47 cases (78.33%) were diagnosed. The intergroup difference was significant (P < 0.05). Clinically, I/Fe3O4 nanometer contrast agent can be used to affect imaging. The detection rate of MRI is higher than that of CT, and the ability to obtain detailed data of occult fractures is better.

On the necessity of an integrative approach to understand protein structural dynamics.

Proteins are dynamic, fluctuating between multiple conformational states. Protein dynamics, spanning orders of magnitude in time and space, allow proteins to perform specific functions. Moreover, under certain conditions, proteins can morph into a different set of conformations. Thus, a complete understanding of protein structural dynamics can provide mechanistic insights into protein function. Here, we review the latest developments in methods used to determine protein ensemble structures and to characterize protein dynamics. Techniques including X-ray crystallography, cryogenic electron microscopy, and small angle scattering can provide structural information on specific conformational states or on the averaged shape of the protein, whereas techniques including nuclear magnetic resonance, fluorescence resonance energy transfer (FRET), and chemical cross-linking coupled with mass spectrometry provide information on the fluctuation of the distances between protein domains, residues, and atoms for the multiple conformational states of the protein. In particular, FRET measurements at the single-molecule level allow rapid resolution of protein conformational states, where information is otherwise obscured in bulk measurements. Taken together, the different techniques complement each other and their integrated use can offer a clear picture of protein structure and dynamics.

Single-molecule tracking of small GTPase Rac1 uncovers spatial regulation of membrane translocation and mechanism for polarized signaling.

Polarized Rac1 signaling is a hallmark of many cellular functions, including cell adhesion, motility, and cell division. The two steps of Rac1 activation are its translocation to the plasma membrane and the exchange of nucleotide from GDP to GTP. It is, however, unclear whether these two processes are regulated independent of each other and what their respective roles are in polarization of Rac1 signaling. We designed a single-particle tracking (SPT) method to quantitatively analyze the kinetics of Rac1 membrane translocation in living cells. We found that the rate of Rac1 translocation was significantly elevated in protrusions during cell spreading on collagen. Furthermore, combining FRET sensor imaging with SPT measurements in the same cell, the recruitment of Rac1 was found to be polarized to an extent similar to that of the nucleotide exchange process. Statistical analysis of single-molecule trajectories and optogenetic manipulation of membrane lipids revealed that Rac1 membrane translocation precedes nucleotide exchange, and is governed primarily by interactions with phospholipids, particularly PI(3,4,5)P3, instead of protein factors. Overall, the study highlights the significance of membrane translocation in spatial Rac1 signaling, which is in addition to the traditional view focusing primarily on GEF distribution and exchange reaction.

The Escherichia coli RNA processing and degradation machinery is compartmentalized within an organized cellular network.

Bacterial RNA processing and degradation involves the co-ordinated action of a large number of RNases, RNA helicases and other proteins. It is not known how this functional network is organized within the cell nor how it is co-ordinated or regulated. In the present study, we show that multiple components of the RNA degradation and processing network of Escherichia coli are localized within extended cellular structures that appear to coil around the periphery of the cell. These include Orn, Hfq, PAP I, RNase III, RppH, RraA and RraB in addition to the previously reported proteins RNase II and RNaseE. Double-label localization studies of several of the proteins showed co-localization of the proteins within the observed structures. Assembly of the proteins into the structures was independent of the MreBCD or MinCDE cytoskeletal systems, RNA synthesis, or nucleoid positioning within the cell. Our results indicate that the components of the RNA processing and degradation network are compartmentalized within the cell rather than diffusely distributed in the cytoplasm. This sequestration provides the cell with a possible mechanism to control access to RNA substrates and to functionally co-ordinate the multiple players of the RNA processing and degradation pathways.

Self-assembly of the bacterial cytoskeleton-associated RNA helicase B protein into polymeric filamentous structures.

The Escherichia coli RNA degradosome proteins are organized into a helical cytoskeletal-like structure within the cell. Here we describe the ATP-dependent assembly of the RhlB component of the degradosome into polymeric filamentous structures in vitro, which suggests that extended polymers of RhlB are likely to comprise a basic core element of the degradosome cytoskeletal structures.

Determination of the fate and contribution of ex vivo expanded human bone marrow stem and progenitor cells for bone formation by 2.3ColGFP.

Bone marrow transplantation can provide an effective cell-based strategy to enhance bone repair. However, the fate of implanted cells and the extent of their contribution to bone osteoinduction remain uncertain. To define the fate of bone marrow-derived cells and their contribution in vivo, we used a bone-specific collagen I promoter (2.3Col) driving green fluorescent protein (GFP) (2.3ColGFP) within a lentiviral vector. Prior to in vivo cell fate determination, we verified a high efficiency of lentiviral transduction in human bone marrow stromal cells (hBMSCs), without altering the proliferation or differentiation potential of these cells. We showed that the 2.3ColGFP marker responded to endogenous transcriptional regulation signals. In a mouse ossicle model, we demonstrated that the 2.3ColGFP marker is able to specifically define human bone marrow-derived stem cells that enter the osteoblast lineage in vivo. In addition, cells labeled with 2.3ColGFP with the donor origin, directly make a major contribution to bone formation. Furthermore, we also demonstrated in a calvarial defect model that a mixture of human bone marrow-derived populations, have stronger bone regenerative potential than that of hBMSCs, and an optimal dose is required for bone regeneration by the mixed populations.

[Study of rhinophysiology on Black people from Africa].

OBJECTIVE: To study the difference of nasal resistance (NR) and nasal parameters between Chinese and Black people from African. METHOD: Nasal minimal cross-sectional area (NMCA), nasal cavity volume (NCV), nasal resistance (NR) in 46 adult Black people (male:29, female: 17) from Africa were tested by ECCOVISION acoustic rhinometry and 50 Chinese (male:25, female:25) were used as contrast. RESULT: NMCA of both Chinese and Black people were positioned at internal nostril. There was significant relationship between the NR and NCV, NR and NMCA. CONCLUSION: The NR is decided by NMCA and NCV. In the same condition, there are different nasal parameters among different race.