Miracle-dz/UniFAR-FTUs huggingface dataset:
Profile of the SeptiCyte™ LAB gene expression assay to diagnose infection in critically ill patients

ABSTRACT Sepsis is a severe and frequently occurring clinical syndrome, caused by the inflammatory response to infections. Recent studies on the human transcriptome during sepsis have yielded several gene-expression assays that might assist physicians during clinical assessment of patients suspected of sepsis. SeptiCyte™ LAB (Immunexpress, Seattle, WA) is the first gene expression assay that was cleared by the FDA in the United States to distinguish infectious from non-infectious causes of systemic inflammation in critically ill patients. The test consists of the simultaneous amplification of four RNA transcripts (CEACAM4, LAMP1, PLAC8, and PLA2G7) in whole blood using a quantitative real-time PCR reaction. This review provides an overview of the challenges in the diagnosis of sepsis, the development of gene expression signatures, and a detailed description of available clinical performance studies evaluating SeptiCyte™ LAB.
Untreated insomnia increases all-cause health care utilization and costs among Medicare beneficiaries

STUDY OBJECTIVES To examine the impact of untreated insomnia on health care utilization (HCU) among a nationally representative sample of Medicare beneficiaries. METHODS Our data source was a random 5% sample of Medicare administrative data for years 2006-2013. Insomnia was operationalized as the presence of at least one claim containing an insomnia-related diagnosis in any given year based on International Classification of Disease, Version 9, Clinical Modification codes or at least one prescription fill for an insomnia-related medication in Part D prescription drug files in each year. We compared HCU in the year prior to insomnia diagnosis to HCU among to non-sleep disordered controls during the same period. RESULTS A total of 151 668 beneficiaries were found to have insomnia. Compared to controls (n = 333 038), beneficiaries with insomnia had higher rates of HCU across all point of service locations. Rates of HCU were highest for inpatient care (rate ratio [RR] 1.61; 95% confidence interval [CI] 1.59, 1.64) and lowest for prescription fills (RR 1.17; 95% CI 1.16, 1.17). Similarly, compared to controls, beneficiaries with insomnia demonstrated $63,607 (95% CI $60,532, $66,685) higher all-cause costs, which were driven primarily by inpatient care ($60,900; 95% CI $56,609, $65,191). Emergency department ($1,492; 95% CI $1,387, $1,596) and prescription costs ($486; 95% CI $454, $518) were also elevated among cases relative to controls. CONCLUSIONS In this randomly selected and nationally representative sample of older Medicare beneficiaries and compared to non-sleep disordered controls, individuals with untreated insomnia demonstrated increased HCU and costs across all points of service.
Overexpression of the Jojoba Aquaporin Gene, ScPIP1, Enhances Drought and Salt Tolerance in Transgenic Arabidopsis

Plasma membrane intrinsic proteins (PIPs) are a subfamily of aquaporin proteins located on plasma membranes where they facilitate the transport of water and small uncharged solutes. PIPs play an important role throughout plant development, and in response to abiotic stresses. Jojoba (Simmondsia chinensis (Link) Schneider), as a typical desert plant, tolerates drought, salinity and nutrient-poor soils. In this study, a PIP1 gene (ScPIP1) was cloned from jojoba and overexpressed in Arabidopsis thaliana. The expression of ScPIP1 at the transcriptional level was induced by polyethylene glycol (PEG) treatment. ScPIP1 overexpressed Arabidopsis plants exhibited higher germination rates, longer roots and higher survival rates compared to the wild-type plants under drought and salt stresses. The results of malonaldehyde (MDA), ion leakage (IL) and proline content measurements indicated that the improved drought and salt tolerance conferred by ScPIP1 was correlated with decreased membrane damage and improved osmotic adjustment. We assume that ScPIP1 may be applied to genetic engineering to improve plant tolerance based on the resistance effect in transgenic Arabidopsis overexpressing ScPIP1.
Modeling Wrist Micromovements to Measure In-Meal Eating Behavior From Inertial Sensor Data

Overweight and obesity are both associated with in-meal eating parameters such as eating speed. Recently, the plethora of available wearable devices in the market ignited the interest of both the scientific community and the industry toward unobtrusive solutions for eating behavior monitoring. In this paper, we present an algorithm for automatically detecting the in-meal food intake cycles using the inertial signals (acceleration and orientation velocity) from an off-the-shelf smartwatch. We use five specific wrist micromovements to model the series of actions leading to and following an intake event (i.e., bite). Food intake detection is performed in two steps. In the first step, we process windows of raw sensor streams and estimate their micromovement probability distributions by means of a convolutional neural network. In the second step, we use a long short-term memory network to capture the temporal evolution and classify sequences of windows as food intake cycles. Evaluation is performed using a challenging dataset of 21 meals from 12 subjects. In our experiments, we compare the performance of our algorithm against three state-of-the-art approaches, where our approach achieves the highest F1 detection score (0.913 in the leave-one-subject-out experiment). The dataset used in the experiments is available at https://mug.ee. auth.gr/intake-cycle-detection/.
A Robust Group-Sparse Representation Variational Method With Applications to Face Recognition

In this paper, we propose a Group-Sparse Representation-based method with applications to Face Recognition (GSR-FR). The novel sparse representation variational model includes a non-convex sparsity-inducing penalty and a robust non-convex loss function. The penalty encourages group sparsity by using an approximation of the $\ell _{0}$ -quasinorm, and the loss function is chosen to make the algorithm robust to noise, occlusions, and disguises. The solution of the non-trivial non-convex optimization problem is efficiently obtained by a majorization-minimization strategy combined with forward-backward splitting, which, in particular, reduces the solution to a sequence of easier convex optimization sub-problems. Extensive experiments on widely used face databases show the potentiality of the proposed model and demonstrate that the GSR-FR algorithm is competitive with the state-of-the-art methods based on sparse representation, especially for very low dimensional feature spaces.
MiR-146a-5p Expression in Peripheral CD14+ Monocytes from Patients with Psoriatic Arthritis Induces Osteoclast Activation, Bone Resorption, and Correlates with Clinical Response

In psoriatic arthritis (PsA), progressive bone destruction is mediated by monocyte-derived osteoclasts. MicroRNAs (miRNAs) regulate many pathophysiological processes; however, their function in PsA patient monocytes has not been examined. This study aims to address whether specific miRNAs in CD14+ monocytes and monocyte-derived osteoclasts cause active osteoclastogenesis in PsA patients. Candidate miRNAs related to monocyte activation (miR-146a-5p, miR-146b-5p and miR-155-5p) were measured in circulatory CD14+ monocytes collected from 34 PsA patients, 17 psoriasis without arthritis (PsO) patients, and 34 normal controls (NCs). CD14+ monocytes were cultured with media containing TNF-α and RANKL to differentiate into osteoclasts. Osteoclast differentiation and bone resorption were measured by TRAP immunostaining and dentin slice resorption, respectively. The results showed that the miR-146a-5p expression was higher in PsA patient-derived CD14+ monocytes compared to PsO and NCs. Activation and bone resorption were selectively enhanced in osteoclasts from PsA patients, but both were abrogated by RNA interference against miR-146a-5p. More importantly, after clinical improvement using biologics, the increased miR-146a-5p expression in CD14+ monocytes from PsA patients was selectively abolished, and associated with blood CRP level. Our findings indicate that miR-146a-5p expression in CD14+ monocytes derived from PsA patients correlates with clinical efficacy, and induction of osteoclast activation and bone resorption.
Characterization of Two New Multidrug-Resistant Strains of Mycobacterium smegmatis: Tools for Routine In Vitro Screening of Novel Anti-Mycobacterial Agents

Mycobacterium tuberculosis is a pathogen of global public health concern. This threat is exacerbated by the emergence of multidrug-resistant and extremely-drug-resistant strains of the pathogen. We have obtained two distinct clones of multidrug-resistant Mycobacterium smegmatis after gradual exposure of Mycobacterium smegmatis mc2 155 to increasing concentrations of erythromycin. The resulting resistant strains of Mycobacterium smegmatis exhibited robust viability in the presence of high concentrations of erythromycin and were found to be resistant to a wide range of other antimicrobials. They also displayed a unique growth phenotype in comparison to the parental drug-susceptible Mycobacterium smegmatis mc2 155, and a distinct colony morphology in the presence of cholesterol. We propose that these two multidrug-resistant clones of Mycobacterium smegmatis could be used as model organisms at the inceptive phase of routine in vitro screening of novel antimicrobial agents targeted against multidrug-resistant Mycobacterial tuberculosis.
Parkin inhibits BAK and BAX apoptotic function by distinct mechanisms during mitophagy

The E3 ubiquitin ligase Parkin is a key effector of the removal of damaged mitochondria by mitophagy. Parkin determines cell fate in response to mitochondrial damage, with its loss promoting early onset Parkinson's disease and potentially also cancer progression. Controlling a cell's apoptotic response is essential to co‐ordinate the removal of damaged mitochondria. We report that following mitochondrial damage‐induced mitophagy, Parkin directly ubiquitinates the apoptotic effector protein BAK at a conserved lysine in its hydrophobic groove, a region that is crucial for BAK activation by BH3‐only proteins and its homo‐dimerisation during apoptosis. Ubiquitination inhibited BAK activity by impairing its activation and the formation of lethal BAK oligomers. Parkin also suppresses BAX‐mediated apoptosis, but in the absence of BAX ubiquitination suggesting an indirect mechanism. In addition, we find that BAK‐dependent mitochondrial outer membrane permeabilisation during apoptosis promotes PINK1‐dependent Parkin activation. Hence, we propose that Parkin directly inhibits BAK to suppress errant apoptosis, thereby allowing the effective clearance of damaged mitochondria, but also promotes clearance of apoptotic mitochondria to limit their potential pro‐inflammatory effect.
Energy expenditure, recovery oxygen consumption, and substrate oxidation during and after body weight resistance exercise with slow movement compared to treadmill walking.

The benefit of body weight resistance exercise with slow movement (BWRE-slow) for muscle function is well-documented, but not for energy metabolism. We aimed to examine physiological responses [e.g., energy expenditure (EE), respiratory exchange ratio (RER), and blood lactate (La)] during and after BWRE-slow compared to EE-matched treadmill walking (TW). Eight healthy young men (23.4 ± 1.8 years old, 171.2 ± 6.2 cm, 63.0 ± 4.8 kg) performed squat, push-up, lunge, heel-raise, hip-lift, and crunch exercises with BWRE-slow modality. Both the concentric and eccentric phases were set to 3 s. A total of three sets (10 repetitions) with 30 s rest between sets were performed for each exercise (26.5 min). On another day, subjects walked on a treadmill for 26.5 min during which EE during exercise was matched to that of BWRE-slow with the researcher controlling the treadmill speed manually. The time course changes of EE and RER were measured. The EE during exercise for BWRE-slow (92.6 ± 16.0 kcal for 26.5 min) was not significantly different from the EE during exercise for TW (95.5 ± 14.1 kcal, p = 0.36). BWRE-slow elicited greater recovery EE (40.55 ± 3.88 kcal for 30 min) than TW (37.61 ± 3.19 kcal, p = 0.029). RER was significantly higher in BWRE-slow during and 0-5 min after exercise, but became significantly lower during 25-30 min after exercise, suggesting greater lipid oxidation was induced about 30 min after exercise in BWRE-slow compared to TW. We also indicated that BWRE-slow has 3.1 metabolic equivalents in average, which is categorized as moderate-intensity physical activity.
Characteristics of Different Types of Childhood Violence and the Risk of Revictimization

This study investigates the relationship between the characteristics of different types of childhood violence and adult victimization using two waves of data from a community telephone survey (T1) and a follow-up survey, including 505 cases and 506 controls, aged 17-35 years (T2). The logistic regression analyses showed that exposure to childhood abuse, regardless of type, was associated with adult victimization. Exposure to multiple types of abuse, victimization both in childhood and in young adulthood, and recency of abuse increased these odds. Our findings emphasize the importance of assessing multiple forms of violence when studying revictimization. Practitioners working with children and young adults should be attentive to the number of victimization types experienced and recent victimization to prevent further abuse.
Impact of Quantum Dot Surface on Complex Formation with Chlorin e6 and Photodynamic Therapy

Nanomaterials have permeated various fields of scientific research, including that of biomedicine, as alternatives for disease diagnosis and therapy. Among different structures, quantum dots (QDs) have distinctive physico-chemical properties sought after in cancer research and eradication. Within the context of cancer therapy, QDs serve the role of transporters and energy donors to photodynamic therapy (PDT) drugs, extending the applicability and efficiency of classic PDT. In contrast to conventional PDT agents, QDs’ surface can be designed to promote cellular targeting and internalization, while their spectral properties enable better light harvesting and deep-tissue use. Here, we investigate the possibility of complex formation between different amphiphilic coating bearing QDs and photosensitizer chlorin e6 (Ce6). We show that complex formation dynamics are dependent on the type of coating—phospholipids or amphiphilic polymers—as well as on the surface charge of QDs. Förster’s resonant energy transfer occurred in every complex studied, confirming the possibility of indirect Ce6 excitation. Nonetheless, in vitro PDT activity was restricted only to negative charge bearing QD-Ce6 complexes, correlating with better accumulation in cancer cells. Overall, these findings help to better design such and similar complexes, as gained insights can be straightforwardly translated to other types of nanostructures—expanding the palette of possible therapeutic agents for cancer therapy.
Mother–infant cortisol attunement: Associations with mother–infant attachment disorganization

Abstract This study explores the conceptualization of mother–infant cortisol attunement both theoretically and empirically, and its association with mother–infant attachment disorganization. In a community sample (N = 256), disorganization and cortisol were assessed during the Strange Situation Procedure (SSP) at infant age 17 months. Salivary cortisol was collected at baseline, and 20 and 40 min after the SSP. We utilized three statistical approaches: correlated growth modeling (probing a simultaneous conceptualization of attunement), cross-lagged modeling (probing a lagged, reciprocal conceptualization of attunement), and a multilevel model difference score analysis (to examine the pattern of discrepancies in mother–infant cortisol values). Correlated growth modeling revealed that disorganized, relative to organized, dyads had significant magnitude of change over time, such that, among disorganized dyads, as mothers had greater declines in cortisol, infants had greater increases. The difference score analysis revealed that disorganized, relative to organized, dyads had a greater divergence between maternal and infant cortisol values, such that maternal values were lower than infant values. Disorganized attachment status was not significantly associated with attunement when conceptualized as reciprocal and lagged in the cross-lagged model. Findings suggest that mother–infant dyads in disorganized attachment relationships, who are by definition behaviorally misattuned, are also misattuned in their adrenocortical responses.
LARGE -SCALE TERRESTRIAL RELAYING OF SATELLITE BROADCASTED REAL -TIME MULTIMEDIA STREAMS

This paper describes an architecture to relay on demand a real-time IP multicast audio-video stream broadcasted by a satellite on a terrestrial link. The stream is received by suitably equipped sites and then relayed to other sites that are not equipped with satellite receiving hardware but are nonetheless willing to receive the stream. By exploiting the properties of satellite transmission and adopting a hybrid satellite/terrestrial, multicast/unicast approach, the described architecture allows to overcome the restrictions suffered by multicast traffic in the global Internet, allowing it to scale easily across autonomous systems. All things considered, the proposed architecture outlines a large-scale interactive audio-video distribution system similar to those based on Content Distribution Networks (CDN) and it compares favorably with them when performances, costs and scalability are examined.
Recommendations for the Initial Cancer Staging MRI Report

Radiology reporting is transitioning from the conventional unstructured, narrative reporting style to the use of templated, structured reports—and to the next level, synoptic reporting, which involves contextual entry options and standardized lexicons. Structured and synoptic forms of reporting can improve both completeness and clarity of reports, which is essential to optimize cancer staging and oncologic patient management. Some other medical specialties have already adopted this approach; for example, in order to achieve and maintain laboratory accreditation from the College of American Pathologists, pathologists must report findings of cancerous specimens in synoptic format. Several standardized systems for reporting and categorizing findings on oncologic imaging staging studies are widely used in radiology, such as BI-RADS (breast lesions), LI-RADS (liver tumors), and PIRADS (prostate cancer); however, most such systems do not address the full range of staging elements and other findings relevant to initial clinical management. Regardless of the report style used, it is useful to review the basic elements that should be included in the magnetic resonance imaging (MRI) report of a patient’s initial MRI staging examination. MRI can provide specific details about tumor staging unobtainable with other imaging methods, and thus has become the preferred imaging method to stage a number of cancers. For most solid tumors, local staging involves determining the elements relevant to the American Joint Committee on Cancer/Tumor-Node-Metastasis or other staging system, as well as those additional features that are essential to the medical, surgical, and/or radiation oncologist for treatment planning. Local staging of the primary tumor site is always required, and distant staging for detection of metastatic deposits is requested based on tumor type and other factors at the time of diagnosis; for hematologic tumors, such as multiple myeloma or lymphoma, initial staging always involves assessment of the entire body. The following elements are recommended for inclusion in the patient’s first MRI staging report.
Scorpion Toxins: Positive Selection at a Distal Site Modulates Functional Evolution at a Bioactive Site

Abstract The bioactive sites of proteins are those that directly interact with their targets. In many immunity- and predation-related proteins, they frequently experience positive selection for dealing with the changes of their targets from competitors. However, some sites that are far away from the interface between proteins and their targets are also identified to evolve under positive selection. Here, we explore the evolutionary implication of such a site in scorpion α-type toxins affecting sodium (Na+) channels (abbreviated as α-ScNaTxs) using a combination of experimental and computational approaches. We found that despite no direct involvement in interaction with Na+ channels, mutations at this site by different types of amino acids led to toxicity change on both rats and insects in three α-ScNaTxs, accompanying differential effects on their structures. Molecular dynamics simulations indicated that the mutations changed the conformational dynamics of the positively selected bioactive site-containing functional regions by allosteric communication, suggesting a potential evolutionary correlation between these bioactive sites and the distant nonbioactive site. Our results reveal for the first time the cause of fast evolution at nonbioactive sites of scorpion neurotoxins, which is presumably to adapt to the change of their bioactive sites through coevolution to maintain an active conformation for channel binding. This might aid rational design of scorpion Na+ channel toxins with improved phyletic selectivity via modification of a distant nonbioactive site.
Ablation and Inhibition of the Immunoproteasome Catalytic Subunit LMP7 Attenuate Experimental Abdominal Aortic Aneurysm Formation in Mice

Low–molecular mass protein 7 (LMP7) is a proteolytic subunit of the immunoproteasome that is involved in regulating inflammatory responses. However, the role of LMP7 in the pathogenesis of abdominal aortic aneurysm (AAA) remains unknown. In this study, ApoE knockout (KO) or LMP7/ApoE double KO (dKO) mice were infused with angiotensin II (Ang II, 1000 ng/kg per minute) for up to 28 d. We found that LMP7 expression was significantly upregulated in AAA tissues from ApoE KO mice and human patients. Moreover, Ang II infusion markedly increased the incidence and severity of AAA in ApoE KO mice, which was considerably reduced in LMP7/ApoE dKO mice. Histological alterations, including aortic wall thickening, collagen deposition, elastin fragmentation, and vascular smooth muscle cell apoptosis in AAA tissue of ApoE KO mice, were also significantly attenuated in LMP7/ApoE dKO mice. Interestingly, LMP7/ApoE dKO mice showed a marked reduction of infiltration of CD3+ T cells, especially CD4+ T cells in AAA tissues compared with ApoE KO mice. Moreover, ablation of LMP7 substantially inhibited the differentiation of CD4+ T cells into Th1 and Th17 cells by reducing the activation of multiple transcriptional factors. We also investigated the effects of an LMP7-specific inhibitor PR-957 (also known as ONX 0914) on AAA formation in ApoE KO mice. PR-957 treatment could reduce the AAA incidence and severity. In conclusion, our results provide, to our knowledge, novel evidence that ablation or pharmacological inhibition of LMP7 attenuates Ang II–induced AAA formation, and LMP7 might be a novel therapeutic target for treating AAA in humans.