Miracle-dz/UniFAR-FTUs huggingface dataset:
Challenges and Strategies for Proteome Analysis of the Interaction of Human Pathogenic Fungi with Host Immune Cells

Opportunistic human pathogenic fungi including the saprotrophic mold Aspergillus fumigatus and the human commensal Candida albicans can cause severe fungal infections in immunocompromised or critically ill patients. The first line of defense against opportunistic fungal pathogens is the innate immune system. Phagocytes such as macrophages, neutrophils and dendritic cells are an important pillar of the innate immune response and have evolved versatile defense strategies against microbial pathogens. On the other hand, human-pathogenic fungi have sophisticated virulence strategies to counteract the innate immune defense. In this context, proteomic approaches can provide deeper insights into the molecular mechanisms of the interaction of host immune cells with fungal pathogens. This is crucial for the identification of both diagnostic biomarkers for fungal infections and therapeutic targets. Studying host-fungal interactions at the protein level is a challenging endeavor, yet there are few studies that have been undertaken. This review draws attention to proteomic techniques and their application to fungal pathogens and to challenges, difficulties, and limitations that may arise in the course of simultaneous dual proteome analysis of host immune cells interacting with diverse morphotypes of fungal pathogens. On this basis, we discuss strategies to overcome these multifaceted experimental and analytical challenges including the viability of immune cells during co-cultivation, the increased and heterogeneous protein complexity of the host proteome dynamically interacting with the fungal proteome, and the demands on normalization strategies in terms of relative quantitative proteome analysis.
Perfect zero-knowledge languages can be recognized in two rounds

A hierarchy of probabilistic complexity classes generalizing NP has recently emerged in the work of [Ba], [GMR], and [GS]. The IP hierarchy is defined through the notion of an interactive proof system, in which an all powerful prover tries to convince a probabilistic polynomial time verifier that a string w is in a language L. The verifier tosses coins and exchanges messages back and forth with the prover before he decides whether to accept w. This proof-system yields "probabilistic" proofs: the verifier may erroneously accept or reject w with small probability. In [GMR] such a protocol was defined to be a zero-knowledge protocol if at the end of the interaction the verifier has learned nothing except that w ∈ L. We study complexity theoretic implications of a language having this property. In particular we prove that if L admits a zeroknowledge proof then L can also be recognized by a two round interactive proof. This complements a result by Fortnow [F] where it is proved that the complement of L has a two round interactive proof protocol. The methods of proof are quite similar to those of Fortnow [F]. As in his case the proof works under the assumption that the original protocol is only zero-knowledge with respect to a specific verifier.
Monitoring bone effect of transdermal hormone replacement therapy by ultrasound investigation at the phalanx: a four-year follow-up study

ObjectiveA controlled 4-year follow-up study was conducted on a population composed of 112 healthy early postmenopausal women to evaluate the ability of ultrasound technology in detecting the effects of hormone replacement therapy (HRT) on bone. At the end of the study, 47 untreated and 25 treated women had been evaluated. Cyclic sequential estrogen/progestogen therapy, 50 &mgr;g/day of transdermal 17&bgr;-estradiol (Rotta Research Laboratorium) plus 5 mg/day of medrogestone (Wyeth-Ayerst) was used. DesignUltrasound transmission through the distal metaphysis of hand phalanxes was measured by DBM Sonic. Beside amplitude-dependent speed of sound (AD-SoS), three new parameters could be calculated: pure speed of sound (pSOS), bone transmission time (BTT), and ultrasound bone profile index (UBPI). Ultrasound measurements were taken at baseline and after 1, 2, and 4 years. ResultsAmong untreated women a significant decrease of all ultrasound parameters was observed at follow-up measurements. In the HRT-treated group we observed a significant increase of AD-SoS, pSoS, and BTT. We qualified as “responders” women in the treated group for whom AD-SoS, pSoS, and BTT increased by more than 2.77 times the coefficient of variation of the measurement, i.e., 95% variability. Women in the treated group were identified as responders at 4 years of follow-up by AD-SoS (56%), pSOS (56%), and BTT (60%). Ultrasound bone profile index declined in both groups, although to a lower extent among HRT-treated subjects. ConclusionsThe 4-year data confirm the results obtained at 1 and 2 years of follow-up. This study demonstrates that bone tissue investigation by ultrasound at the phalanx can be used to monitor the effect of HRT, and thus it should be considered a potential technology for the management of menopause by gynecologists.
Connecting lignin-degradation pathway with pre-treatment inhibitor sensitivity of Cupriavidus necator

To produce lignocellulosic biofuels economically, the complete release of monomers from the plant cell wall components, cellulose, hemicellulose, and lignin, through pre-treatment and hydrolysis (both enzymatic and chemical), and the efficient utilization of these monomers as carbon sources, is crucial. In addition, the identification and development of robust microbial biofuel production strains that can tolerate the toxic compounds generated during pre-treatment and hydrolysis is also essential. In this work, Cupriavidus necator was selected due to its capabilities for utilizing lignin monomers and producing polyhydroxylbutyrate (PHB), a bioplastic as well as an advanced biofuel intermediate. We characterized the growth kinetics of C. necator in pre-treated corn stover slurry as well as individually in the pre-sence of 11 potentially toxic compounds in the saccharified slurry. We found that C. necator was sensitive to the saccharified slurry produced from dilute acid pre-treated corn stover. Five out of 11 compounds within the slurry were characterized as toxic to C. necator, namely ammonium acetate, furfural, hydroxymethylfurfural (HMF), benzoic acid, and p-coumaric acid. Aldehydes (e.g., furfural and HMF) were more toxic than the acetate and the lignin degradation products benzoic acid and p-coumaric acid; furfural was identified as the most toxic compound. Although toxic to C. necator at high concentration, ammonium acetate, benzoic acid, and p-coumaric acid could be utilized by C. necator with a stimulating effect on C. necator growth. Consequently, the lignin degradation pathway of C. necator was reconstructed based on genomic information and literature. The efficient conversion of intermediate catechol to downstream products of cis,cis-muconate or 2-hydroxymuconate-6-semialdehyde may help improve the robustness of C. necator to benzoic acid and p-coumaric acid as well as improve PHB productivity.
K-clustered tensor approximation: A sparse multilinear model for real-time rendering

With the increasing demands for photo-realistic image synthesis in real time, we propose a sparse multilinear model, which is named K-Clustered Tensor Approximation (K-CTA), to efficiently analyze and approximate large-scale multidimensional visual datasets, so that both storage space and rendering time are substantially reduced. K-CTA not only extends previous work on Clustered Tensor Approximation (CTA) to exploit inter-cluster coherence, but also allows a compact and sparse representation for high-dimensional datasets with just a few low-order factors and reduced multidimensional cluster core tensors. Thus, K-CTA can be regarded as a sparse extension of CTA and a multilinear generalization of sparse representation. Experimental results demonstrate that K-CTA can accurately approximate spatially varying visual datasets, such as bidirectional texture functions, view-dependent occlusion texture functions, and biscale radiance transfer functions for efficient rendering in real-time applications.
Malaria Parasite Detection From Peripheral Blood Smear Images Using Deep Belief Networks

In this paper, we propose a novel method to identify the presence of malaria parasites in human peripheral blood smear images using a deep belief network (DBN). This paper introduces a trained model based on a DBN to classify 4100 peripheral blood smear images into the parasite or non-parasite class. The proposed DBN is pre-trained by stacking restricted Boltzmann machines using the contrastive divergence method for pre-training. To train the DBN, we extract features from the images and initialize the visible variables of the DBN. A concatenated feature of color and texture is used as a feature vector in this paper. Finally, the DBN is discriminatively fine-tuned using a backpropagation algorithm that computes the probability of class labels. The optimum size of the DBN architecture used in this paper is 484-600-600-600-600-2, in which the visible layer has 484 nodes and the output layer has two nodes with four hidden layers containing 600 hidden nodes in every layer. The proposed method has performed significantly better than the other state-of-the-art methods with an F-score of 89.66%, a sensitivity of 97.60%, and specificity of 95.92%. This paper is the first application of a DBN for malaria parasite detection in human peripheral blood smear images.
Cochlear nerve diameter in normal hearing ears using high‐resolution magnetic resonance imaging

Deficient cochlear nerves (CN) have been associated with poor cochlear implant performance. Normative data on CN diameter based on radiographic imaging have not been published. The objectives of this study were to determine if CN diameter could be reproducibly measured on parasagittal constructive interference in steady state (CISS)‐sequence magnetic resonance imaging (MRI) and to establish a normative range for CN diameter.
Hepatic and systemic haemodynamic changes after MARS in patients with acute on chronic liver failure

Abstract Hyperdynamic circulation and portal hypertension characterize acute on chronic liver failure (AoCLF), partially because of circulating mediators. Molecular Absorbents Recirculating System (MARS) may remove some of these substances. The objective of this study was to evaluate the effect of MARS on portal pressure, systemic haemodynamic and endogenous vasoactive systems. MARS treatment was performed in four patients with AoCLF (mean age 36.2 ± 3.1 years; Child–Pugh C 11 ± 1.8 points; three AAH and one NASH). Systemic and splanchnic haemodynamic measurements were performed before and after each session. Plasmatic renin activity (PRA) and NE were measured at baseline, at the end of the sessions and 10 days after MARS. All patients had severe portal hypertension (HVPG = 23 ± 7 mmHg) and pronounced hyperdynamic circulation (MAP 77.8 ± 11.7 mmHg; CO 11.2 ± 1.6 L/min; SVRI 478.5 ± 105 dyne s/cm5). HVPG decreased at the end of the first session in all patients (23 ± 7 mmHg vs 17.3 ± 9.9 mmHg; P = 0.05; mean decrease 32 ± 24%) because of a decrease in WHVP (40.7 ± 5.6 mmHg vs 34 ± 9.6 mmHg; P = 0.025; mean decrease 18 ± 19%). MARS significantly attenuated hyperdynamic circulation as shown by a decrease in CO (11.2 ± 1.6 L/min vs 9.4 ± 2.1 L/min; mean decrease 12.3%), with an increase in MAP (77.8 ± 11.7 mmHg vs 84.2 ± 8 mmHg; mean increase 9.2%) and in SVRI (478.5 ± 105 dyne s/cm5 vs 622 ± 198 dyne s/cm5; mean increase 41%). PRA and NE decreased significantly (14.2 ± 17.2 ng/mL/h vs 3.7 ± 3.4 ng/mL/h; 1319 ± 1002 pg/mL vs 617 ± 260 pg/mL, respectively). The NE decrease was correlated to HVPG decrease (r = 1, P = 0.01). MARS decreases portal hypertension and ameliorates hyperdynamic circulation in patients with AoCLF, probably mediated by clearance of vasoactive substances. Further studies are necessary to confirm these results.
Aging and Estrogen Status: A Possible Endothelium-Dependent Vascular Coupling Mechanism in Bone Remodeling

Bone loss with aging and menopause may be linked to vascular endothelial dysfunction. The purpose of the study was to determine whether putative modifications in endothelium-dependent vasodilation of the principal nutrient artery (PNA) of the femur are associated with changes in trabecular bone volume (BV/TV) with altered estrogen status in young (6 mon) and old (24 mon) female Fischer-344 rats. Animals were divided into 6 groups: 1) young intact, 2) old intact, 3) young ovariectomized (OVX), 4) old OVX, 5) young OVX plus estrogen replacement (OVX+E2), and 6) old OVX+E2. PNA endothelium-dependent vasodilation was assessed in vitro using acetylcholine. Trabecular bone volume of the distal femoral metaphysis was determined by microCT. In young rats, vasodilation was diminished by OVX and restored with estrogen replacement (intact, 82±7; OVX, 61±9; OVX+E2, 90±4%), which corresponded with similar modifications in BV/TV (intact, 28.7±1.6; OVX, 16.3±0.9; OVX+E2, 25.7±1.4%). In old animals, vasodilation was unaffected by OVX but enhanced with estrogen replacement (intact, 55±8; OVX, 59±7; OVX+E2, 92±4%). Likewise, modifications in BV/TV followed the same pattern (intact, 33.1±1.6; OVX, 34.4±3.7; OVX+E2, 42.4±2.1%). Furthermore, in old animals with low endogenous estrogen (i.e., intact and old OVX), vasodilation was correlated with BV/TV (R2 = 0.630; P<0.001). These data demonstrate parallel effects of estrogen on vascular endothelial function and BV/TV, and provide for a possible coupling mechanism linking endothelium-dependent vasodilation to bone remodeling.
THE DiskMass SURVEY. III. STELLAR KINEMATICS VIA CROSS-CORRELATION

We describe a new cross-correlation (CC) approach used by our survey to derive stellar kinematics from galaxy-continuum spectroscopy. This approach adopts the formal error analysis derived by Statler, but properly handles spectral masks. Thus, we address the primary concerns regarding application of the CC method to censored data, while maintaining its primary advantage by consolidating kinematic and template-mismatch information toward different regions of the CC function. We identify a systematic error in the nominal CC method of approximately 10% in velocity dispersion incurred by a mistreatment of detector-censored data, which is eliminated by our new method. We derive our approach from first principles, and we use Monte Carlo simulations to demonstrate its efficacy. An identical set of Monte Carlo simulations performed using the well-established penalized-pixel-fitting code of Cappellari & Emsellem compares favorably with the results from our newly implemented software. Finally, we provide a practical demonstration of this software by extracting stellar kinematics from SparsePak spectra of UGC 6918.
Peace and War

In the study reported here, we examined posttraumatic stress disorder (PTSD) symptoms in 746 Danish soldiers measured on five occasions before, during, and after deployment to Afghanistan. Using latent class growth analysis, we identified six trajectories of change in PTSD symptoms. Two resilient trajectories had low levels across all five times, and a new-onset trajectory started low and showed a marked increase of PTSD symptoms. Three temporary-benefit trajectories, not previously described in the literature, showed decreases in PTSD symptoms during (or immediately after) deployment, followed by increases after return from deployment. Predeployment emotional problems and predeployment traumas, especially childhood adversities, were predictors for inclusion in the nonresilient trajectories, whereas deployment-related stress was not. These findings challenge standard views of PTSD in two ways. First, they show that factors other than immediately preceding stressors are critical for PTSD development, with childhood adversities being central. Second, they demonstrate that the development of PTSD symptoms shows heterogeneity, which indicates the need for multiple measurements to understand PTSD and identify people in need of treatment.
On the SPARQL Direct Semantics Entailment Regime for OWL 2 QL

OWL 2 QL is the profile of OWL 2 targeted to Ontology-Based Data Access (OBDA) scenarios, where large amount of data are to be accessed and thus query answering is required to be especially efficient in the size of such data, namely AC0 in data complexity. On the other hand, the syntax and the semantics of the SPARQL query language for OWL 2 is defined by means of the Direct Semantics Entailment Regime (DSER), which considers queries including any assertion expressible in the language of the queried ontology, i.e., both ABox atoms, TBox atoms and inequalities expressed by means of DifferentIndividuals atoms. Thus, in this paper, we investigate query answering over OWL 2 QL under DSER. In particular, we show that, by virtue of the restricted meaning assigned to existential variables and union, query answering can be reduced to the evaluation of a Datalog program. Finally, we investigate query answering under a new SPARQL entailment regime, called Direct Semantics Answering Regime (DSAR), obtained by modifying DSER in such a way that existentially quantified variables are assigned the classical logical meaning, and provide an algorithm for answering queries over OWL 2 QL ontologies under DSAR, that is AC0 in data complexity, for a class of queries comprising both TBox atoms, ABox atoms and inequalities.
Resource Allocation Techniques for Wireless Powered Communication Networks With Energy Storage Constraint

This paper studies multiuser wireless powered communication networks, where energy constrained users charge their energy storages by scavenging energy of the radio frequency signals radiated from a hybrid access point (H-AP). The energy is then utilized for the users' uplink information transmission to the H-AP in time division multiple access mode. In this system, we aim to maximize the uplink sum rate performance by jointly optimizing energy and time resource allocation for multiple users in both infinite capacity and finite capacity energy storage cases. First, when the users are equipped with the infinite capacity energy storages, we derive the optimal downlink energy transmission policy at the H-AP. Based on this result, analytical resource allocation solutions are obtained. Next, we propose the optimal energy and time allocation algorithm for the case where each user has finite capacity energy storage. Simulation results confirm that the proposed algorithms offer about 30% average sum rate performance gain over conventional schemes.
Physical education can improve insulin resistance: the LOOK randomized cluster trial.

PURPOSE As impaired glucose metabolism may arise progressively during childhood, we sought to determine whether the introduction of specialist-taught school physical education (PE) based on sound educational principles could improve insulin resistance (IR) in elementary school children. METHODS In this 4-yr cluster-randomized intervention study, participants were 367 boys and 341 girls (mean age = 8.1 yr, SD = 0.35) initially in grade 2 in 29 elementary schools situated in suburbs of similar socioeconomic status. In 13 schools, 100 min·wk-1 of PE, usually conducted by general classroom teachers, was replaced with two classes per week taught by visiting specialist PE teachers; the remaining schools formed the control group. Teacher and pupil behavior were recorded, and measurements in grades 2, 4, and 6 included fasting blood glucose and insulin to calculate the homeostatic model of IR, percent body fat, physical activity, fitness, and pubertal development. RESULTS On average, the intervention PE classes included more fitness work than the control PE classes (7 vs 1 min, P < 0.001) and more moderate physical activity (17 vs 10 min, P < 0.001). With no differences at baseline, by grade 6, the intervention had lowered IR by 14% (95% confidence interval = 1%-31%) in the boys and by 9% (95% confidence interval = 5%-26%) in the girls, and the percentage of children with IR greater than 3, a cutoff point for metabolic risk, was lower in the intervention than the control group (combined, 22% vs 31%, P = 0.03; boys, 12% vs 21%, P = 0.06; girls, 32% vs 40%, P = 0.05). CONCLUSIONS Specialist-taught primary school PE improved IR in community-based children, thereby offering a primordial preventative strategy that could be coordinated widely although a school-based approach.
SUBJECTIVE CERAMIC MACHINABILITY AND MATERIAL PROPERTIES

Nine different ceramic materials were subjectively evaluated, on a scale from 1 to 100, for machinability by experienced machinists. The property values of hardness, fracture toughness and elastic modulus were also obtained for the materials. Correlations were sought between the material properties and subjective machinability results. A grindability parameter and a model predicting material removal rates were included in the correlation analyses. Trends were noted between the subjective machinability evaluations and both hardness and grindability, although the grindability parameter did not correlate with either hardness or the material removal rate model.
Distortion analysis of switched-current circuits

A distortion analysis based on the large signal behavior of the basic switched-current memory cell is presented. In the first part, based on a closed form solution of the step response, distortion due to the settling error is addressed. In the second part, distortion caused by clock-feedthrough is analysed. The solutions are compared with simulated and/or measured results. Furthermore, harmonic terms above the fifth are shown to be negligible.
Takotsubo Cardiomyopathy: A Case of Persistent Apical Ballooning Complicated by an Apical Mural Thrombus

Takotsubo cardiomyopathy (TTC) is an infrequent cardiac syndrome characterized by acute onset chest pain with apical ballooning on echocardiography. It is often triggered by severe emotional or physical stress, and in contrast to acute myocardial infarction (AMI), the regional wall motion abnormality returns to normal within days. Here, we describe a 62-year-old female who presented with acute onset chest pain during treatment for a liver abscess. We presumed a diagnosis of AMI because of ST segment elevation on electrocardiography and elevated cardiac enzyme levels. However, the patient's coronary arteries were normal on angiography, and apical ballooning was seen on echocardiography. A diagnosis of TTC was made, and the patient was managed with intensive cardiopulmonary support using vasopressors in our hospital's medical intensive care unit. The patient's symptoms improved, but persistent severe left ventricular dysfunction was detected on follow-up echocardiography. After 5 weeks, a new apical mural thrombus appeared, and anticoagulation therapy was started. The apical ballooning persisted 3 months later, although the patient's overall ejection fraction was slightly improved. The apical thrombus was completely resolved without any embolic event. Non-adrenergic inotropics can be recommended in TTC with shock, and clinicians should keep in mind the potential risk of thrombus formation and cardioembolism.