Miracle-dz/UniFAR-FTUs huggingface dataset:
Three‐dimensional structure of Mycoplasma pneumoniae’s attachment organelle and a model for its role in gliding motility

While most motile bacteria propel themselves with flagella, other mechanisms have been described including retraction of surface‐attached pili, secretion of polysaccharides, or movement of motors along surface protein tracks. These have been referred to collectively as forms of ‘gliding’ motility. Despite being simultaneously one of the smallest and simplest of all known cells, Mycoplasma pneumoniae builds a surprisingly large and complex cell extension known as the attachment organelle that enables it to glide. Here, three‐dimensional images of the attachment organelle were produced with unprecedented clarity and authenticity using state‐of‐the‐art electron cryotomography. The attachment organelle was seen to contain a multisubunit, jointed, dynamic motor much larger than a flagellar basal body and comparable in complexity. A new model for its function is proposed wherein inchworm‐like conformational changes of its electron‐dense core are leveraged against a cytoplasmic anchor and transmitted to the surface through layered adhesion proteins.
Leatherbacks Swimming In Silico: Modeling and Verifying Their Momentum and Heat Balance Using Computational Fluid Dynamics

As global temperatures increase throughout the coming decades, species ranges will shift. New combinations of abiotic conditions will make predicting these range shifts difficult. Biophysical mechanistic niche modeling places bounds on an animal’s niche through analyzing the animal’s physical interactions with the environment. Biophysical mechanistic niche modeling is flexible enough to accommodate these new combinations of abiotic conditions. However, this approach is difficult to implement for aquatic species because of complex interactions among thrust, metabolic rate and heat transfer. We use contemporary computational fluid dynamic techniques to overcome these difficulties. We model the complex 3D motion of a swimming neonate and juvenile leatherback sea turtle to find power and heat transfer rates during the stroke. We combine the results from these simulations and a numerical model to accurately predict the core temperature of a swimming leatherback. These results are the first steps in developing a highly accurate mechanistic niche model, which can assists paleontologist in understanding biogeographic shifts as well as aid contemporary species managers about potential range shifts over the coming decades.
Modularity and centrality in an sRNA network

Small RNAs (sRNAs) are small, non-coding RNA species that control numerous cellular processes, and they are important components of post-transcriptional regulation. We study an sRNA network in the present paper, emphasis has been focused on modularity and centrality in the sRNA network. We engage a link clustering method for analyzing the sRNA network, and identify biologically functional modules and key genes in the sRNA network.
Binding of Shiga Toxin 2e to Porcine Erythrocytes In Vivo and In Vitro

ABSTRACT Shiga toxin 2e (Stx2e), produced by host-adapted Shiga toxin-producing Escherichia coli (STEC) strains, causes edema disease in weaned pigs. Edema disease is manifested as vascular necrosis, edema, neurologic signs, and death. In this study we sought to determine the correlation between the presence of Stx2e in the blood of STEC-inoculated pigs and the disease outcome. Eleven of 15 (73%) pigs with clinical and 5 of 35 (14%) pigs with subclinical edema disease had detectable levels of Stx2e in the red-blood-cell (RBC) fraction of their blood but not in serum or plasma. The presence of Stx2e in the RBC fraction was strongly associated with the development of clinical disease (relative risk, 5.8; P < 0.0001). Subclinical pigs with Stx2e in their blood developed more-extensive vascular lesions than pigs without detectable Stx2e in their blood (average proportions of necrotic arterioles, 63 and 27.5%, respectively; P = 0.001). Variations in RBC-bound Stx2e levels could in part reflect variations in the binding capacity of RBCs. As an initial step toward addressing this possibility, assays were conducted to determine if pigs vary in the Stx2e binding capacity of their RBCs. An in vitro study of noninoculated pigs demonstrated two phenotypes based on the capacity of the RBCs to bind Stx2e. While RBCs from most of the pigs consistently bound high levels of Stx2e (high-binding phenotype), consistently low Stx2e binding was detected in RBCs from a few pigs (low-binding phenotype). The low- and high-binding phenotypes of individual pigs remained consistent throughout repeated samplings over 2 months.
Do children with dyslexia and/or specific language impairment compensate for place assimilation? Insight into phonological grammar and representations

English speakers have to recognize, for example, that te[m] in te[m] pens is a form of ten, despite place assimilation of the nasal consonant. Children with dyslexia and specific language impairment (SLI) are commonly proposed to have a phonological deficit, and we investigate whether that deficit extends to place assimilation, as a way of probing phonological representations and phonological grammar. Children with SLI plus dyslexia, SLI only, and dyslexia only listened to sentences containing a target word in different assimilatory contexts—viable, unviable, and no change—and pressed a button to report hearing the target. The dyslexia-only group did not differ from age-matched controls, but the SLI groups showed more limited ability to accurately identify words within sentences. Once this factor was taken into account, the groups did not differ in their ability to compensate for assimilation. The results add to a growing body of evidence that phonological representations are not necessarily impaired in dyslexia. SLI children's results suggest that they too are sensitive to this aspect of phonological grammar, but are more liberal in their acceptance of alternative phonological forms of words. Furthermore, these children's ability to reject alternative phonological forms seems to be primarily limited by their vocabulary size and phonological awareness abilities.
The shading probe: fast appearance acquisition for mobile AR

The ubiquity of mobile devices with powerful processors and integrated video cameras is re-opening the discussion on practical augmented reality (AR). Despite this technological convergence, several issues prevent reliable and immersive AR on these platforms. We address one such problem, the shading of virtual objects and determination of lighting that remains consistent with the surrounding environment. We design a novel light probe and exploit its structure to permit an efficient reformulation of the rendering equation that is suitable for fast shading on mobile devices. Unlike prior approaches, our shading probe directly captures the shading, and not the incident light, in a scene. As such, we avoid costly and unreliable radiometric calibration as well as side-stepping the need for complex shading algorithms. Moreover, we can tailor the shading probe's structure to better handle common lighting scenarios, such as outdoor settings. We achieve high-performance shading of virtual objects in an AR context, incorporating plausible local global-illumination effects, on mobile platforms.
A model for mining relevant and non-redundant information

We propose a relatively simple yet powerful model for choosing relevant and non-redundant pieces of information. The model addresses data mining or information retrieval settings where relevance is measured with respect to a set of key or query objects, either specified by the user or obtained by a data mining step. The problem addressed is not only to identify other relevant objects, but also ensure that they are not related to possible negative query objects, and that they are not redundant with respect to each other. The model proposed here only assumes a similarity or distance function for the objects. It has simple parameterization to allow for different behaviors with respect to query objects. We analyze the model and give two efficient, approximate methods. We illustrate and evaluate the proposed model on different applications: linguistics and social networks. The results indicate that the model and methods are useful in finding a relevant and non-redundant set of results. While this area has been a popular topic of research, our contribution is to provide a simple, generic model that covers several related approaches while providing a systematic model for taking account of positive and negative query objects as well as non-redundancy of the output.
Preoperative management of patients undergoing liver resection for perihilar cholangiocarcinoma

Surgical resection with negative margins is the standard treatment for perihilar cholangiocarcinoma whenever possible. Patient’s frequent low performance status at presentation and need of extended resections require optimization of the patient’s condition in the preoperative setting. Biliary drainage is mandatory in case of cholangitis, jaundice-related liver insufficiency, malnutrition or renal failure. Drainage is also necessary in case of portal vein embolization (PVE), in order to improve regeneration of the future liver remnant (FLR). Unilateral drainage of the FLR should be obtained, while bilateral drainage is required in case of cholangitis, slow reduction in bilirubin and uncertainty about the side of resection. The technique for biliary drainage should be decided according to the local expertise and other factors (need of further evaluation of tumour extension, patient’s compliance, necessity of bilateral drainage). Preoperative symbiotics-reduce postoperative infections. PVE is safe and increases the safety of surgery in case of extended liver resections. It is indicated in case of low FLR volume (<40%), low FLR function or in case of previous cholangitis. ALPPS is not recommended in case of PHC.
Baxter Q-operator and Givental integral representation for C_n and D_n

Recently integral representations for the eigenfunctions of quadratic open Toda chain Hamiltonians for classical groups was proposed. This representation generalizes Givental representation for A_n. In this note we verify that the wave functions defined by these integral representations are common eigenfunctions for the complete set of open Toda chain Hamiltonians. We consider the zero eigenvalue wave functions for classical groups C_n and D_n thus completing the generalization of the Givental construction in these cases. The construction is based on a recursive procedure and uses the formalism of Baxter Q-operators. We also verify that the integral Q-operators for C_n, D_n and twisted affine algebra A_{2n-1}^{(2)} proposed previously intertwine complete sets of Hamiltonian operators. Finally we provide integral representations of the eigenfunctions of the quadratic $D_n$ Toda chain Hamiltonians for generic nonzero eigenvalues.
Cascade model predictive control of a PMSM with periodic disturbance rejection

This paper develops a cascade Model Predictive Control (MPC) structure to provide speed control for a Permanent Magnet Synchronous Motor (PMSM). The MPC design is based on the linearized per unit model of the nonlinear PMSM dynamics. Hildreth's procedure is employed to solve the quadratic programming problem with constraints imposed. The extension of MPC to include more frequency modes for the application of periodic disturbance rejection due to the current sensor offset is also described. Finally, an illustrative simulation example is given.
Effect of Tibolone on Breast Cancer Cell Proliferation in Postmenopausal ER+ Patients: Results from STEM Trial

Purpose: Tibolone is a selective tissue estrogenic activity regulator, approved for the treatment of vasomotor symptoms in postmenopausal women. We have done an exploratory, double-blind, randomized, placebo-controlled pilot trial to investigate the tissue-specific effects of 2.5 mg tibolone on breast cancer in postmenopausal women, in particular on tissue proliferation (STEM, Study of Tibolone Effects on Mamma carcinoma tissue). Experimental Design: Postmenopausal women with initially stage I/II, estrogen receptor–positive (ER+) primary breast cancer, were randomly assigned to 14 days of placebo or 2.5 mg/d tibolone. Core biopsies of the primary tumor were obtained before and after treatment. Ki-67 and apoptosis index were analyzed in baseline and corresponding posttreatment specimen. Results: Of 102 enrolled patients, 95 had evaluable data. Baseline characteristics were comparable between both treatment groups. Breast cancer cases are mainly invasive (99%), stage I or II (42% and 50% respectively), and ER+ (99%). Median intratumoral Ki-67 expression at baseline was 13.0% in the tibolone group and 17.8% in the placebo group, and decreased to 12.0% after 14 days of tibolone while increasing to 19.0% in the placebo group. This change from baseline was not significantly different between tibolone and placebo (Wilcoxon test; P = 0.17). A significant difference was observed between the treatment groups when the median change from baseline apoptosis index was compared between the treatment groups (tibolone, 0.0%; placebo, +0.3%; Wilcoxon test; P = 0.031). The incidence of adverse effects was comparable. Conclusions: In ER+ breast tumors, 2.5 mg/d tibolone given for 14 days has no significant effect on tumor cell proliferation.
Magnetic resonance imaging evidence of decreased putamenal iron content in idiopathic Parkinson's disease.

OBJECTIVE To determine the changes in basal ganglia iron content associated with various stages of idiopathic Parkinson's disease. DESIGN Prospective magnetic resonance imaging study using a 2-T magnet. SETTING Ambulatory care referral center. PATIENTS AND PARTICIPANTS Forty-five patients suffering from levodopa-responsive Parkinson's disease and 45 age-matched controls. MAIN OUTCOME MEASURES The T2 relaxation time calculated in various regions of the basal ganglia, the duration of Parkinson's disease, and the age of subjects. RESULTS Patients with Parkinson's disease exhibited significantly decreased T2 relaxation time in the pars compacta of the substantia nigra compared with controls (P < .01), regardless of disease duration. Patients with a duration of illness above 10 years (n = 12) exhibited significantly increased T2 relaxation time in the anterior and posterior putamen (P < .005 and P < .01, respectively) and in the pallidum (P < .05) compared with age-matched controls. Putamental T2 relaxation time positively correlated with disease duration (P < .05). CONCLUSION These results suggest that more complex brain iron changes than those previously reported are associated with idiopathic Parkinson's disease, including increased nigral iron content and decreased putamenal and pallidal iron concentration in patients with a duration of illness above 10 years.
A review of real-time EEG sonification research

Over the last few decades there has been steady growth in research that addresses the real-time sonification of electroencephalographic (EEG) data. Diverse application areas include medical data screening, Brain Computer Interfaces (BCI), neurofeedback, affective computing and applications in the arts. The present paper presents an overview and critical review of the principal research to date in EEG data sonification. Firstly, we identify several sub-domains of real-time EEG sonification and discuss their diverse approaches and goals. Secondly, we describe our search and inclusion criteria, and then present a synoptic summary table spanning over fifty different research projects or published research findings. Thirdly, we analyze sonification approaches to the various EEG data dimensions such as time-frequency filtering, signal level, location, before going on to consider higher order EEG features. Finally, we discuss future application domains which may benefit from new capabilities in the real-time sonification of EEG data. We believe that the present critical review may help to reduce research fragmentation and may aid future collaboration in this emerging multidisciplinary area.
A holistic framework for the fostering of an information security sub-culture in organizations

Modern businesses operates in an emerging global information society. In this information society it is imperative for modern organizations to take the protection of their information resources seriously. This protection of information resources is to a large extent dependent on human co-operated behavior. This human factor is the weakest link in information security, and consists of two interrelated dimensions. Firstly, employees must have sufficient knowledge about information security in order to effectively implement, and maintain, the various information security controls. Secondly, the employees must have the correct attitude towards information security. These two dimensions to the human factor in information security are closely related, and to a degree co-dependent upon each other. It would thus make sense to address these dimensions holistically. This paper combines previously proposed principles and methodologies into a single holistic framework that addresses both the dimensions to this human factor in information security.
Customized probability models for early severe sepsis in adult intensive care patients. Intensive Care Unit Scoring Group.

OBJECTIVE To develop customized versions of the Simplified Acute Physiology Score II (SAPS II) and the 24-hour Mortality Probability Model II (MPM II) to estimate the probability of mortality for intensive care unit patients with early severe sepsis. DESIGN AND SETTING Logistic regression models developed for patients with severe sepsis in a database of adult medical and surgical intensive care units in 12 countries. PATIENTS Of 11,458 patients in the intensive care unit for at least 24 hours, 1130 had severe sepsis based on criteria of the American College of Chest Physicians and the Society of Critical Care Medicine (systemic inflammatory response syndrome in response to infection, plus hypotension, hypoperfusion, or multiple organ dysfunction). RESULTS In patients with severe sepsis, mortality was higher (48.0% vs 19.6% among other patients) and 28-day survival was lower. The customized SAPS II was well calibrated (P = .92 for the goodness-of-fit test) and discriminated well (area under the receiver operating characteristic [ROC] curve, 0.78). Performance in the validation sample was equally good (P = .85 for the goodness-of-fit test; area under the ROC curve, 0.79). The customized MPM II was well calibrated (P = .92 for the goodness-of-fit test) and discriminated well (area under the ROC curve, 0.79). Performance in the validation sample was equally good (P = .52 for the goodness-of-fit test; area under the ROC curve, 0.75). The models are independent of each other; either can be used alone to estimate the probability of mortality of patients with severe sepsis. CONCLUSIONS Customization provides a simple technique to apply existing models to a subgroup of patients. Accurately assessing the probability of hospital mortality is a useful adjunct for clinical trials.
Tracking the performance of an R&D programme in the Biomedical Sciences

This article aims at offering an evaluation framework of an RD however, an increase in the share of papers mention is observed 2 years after it was launched. We suggest that by finding the point at which the share of mentions stabilizes may be a good strategy to identify the complete fulfilment of these types of R&D policies.
Manifold regularized robust unsupervised feature selection for image clustering

Dimensionality reduction is a challenging task for high dimensional data processing in machine learning and data mining. As an effective dimension reduction technique, unsupervised feature selection aims at finding a subset of features to retain the most relevant information. In this paper, we propose a novel unsupervised feature selection method, called Manifold Regularized Robust Unsupervised Feature Selection (MRUFS) for image clustering. MRUFS performs robust discriminative feature selection and robust clustering simultaneously under ℓ_2,1-norm while preserves the local manifold structures of original data. Compared with several unsupervised feature selection methods, the proposed algorithm comes with better clustering performance for two datasets: FERET and COIL20 which we have experimented with here.
Mitochondrial Morphology and Function of the Pancreatic β-Cells INS-1 Model upon Chronic Exposure to Sub-Lethal Cadmium Doses

The impact of chronic cadmium exposure and slow accumulation on the occurrence and development of diabetes is controversial for human populations. Islets of Langerhans play a prominent role in the etiology of the disease, including by their ability to secrete insulin. Conversion of glucose increase into insulin secretion involves mitochondria. A rat model of pancreatic β-cells was exposed to largely sub-lethal levels of cadmium cations applied for the longest possible time. Cadmium entered cells at concentrations far below those inducing cell death and accumulated by factors reaching several hundred folds the basal level. The mitochondria reorganized in response to the challenge by favoring fission as measured by increased circularity at cadmium levels already ten-fold below the median lethal dose. However, the energy charge and respiratory flux devoted to adenosine triphosphate synthesis were only affected at the onset of cellular death. The present data indicate that mitochondria participate in the adaptation of β-cells to even a moderate cadmium burden without losing functionality, but their impairment in the long run may contribute to cellular dysfunction, when viability and β-cells mass are affected as observed in diabetes.
Transforming growth factor-β employs HMGA2 to elicit epithelial–mesenchymal transition

Epithelial–mesenchymal transition (EMT) occurs during embryogenesis, carcinoma invasiveness, and metastasis and can be elicited by transforming growth factor-β (TGF-β) signaling via intracellular Smad transducers. The molecular mechanisms that control the onset of EMT remain largely unexplored. Transcriptomic analysis revealed that the high mobility group A2 (HMGA2) gene is induced by the Smad pathway during EMT. Endogenous HMGA2 mediates EMT by TGF-β, whereas ectopic HMGA2 causes irreversible EMT characterized by severe E-cadherin suppression. HMGA2 provides transcriptional input for the expression control of four known regulators of EMT, the zinc-finger proteins Snail and Slug, the basic helix-loop-helix protein Twist, and inhibitor of differentiation 2. We delineate a pathway that links TGF-β signaling to the control of epithelial differentiation via HMGA2 and a cohort of major regulators of tumor invasiveness and metastasis. This network of signaling/transcription factors that work sequentially to establish EMT suggests that combinatorial detection of these proteins could serve as a new tool for EMT analysis in cancer patients.