Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellular Responses of the Lichen Circinaria gyrosa in Mars-Like Conditions

Lichens are extremely resistant organisms that colonize harsh climatic areas, some of them defined as “Mars-analog sites. ” There still remain many unsolved questions as to how lichens survive under such extreme conditions. Several studies have been performed to test the resistance of various lichen species under space and in simulated Mars-like conditions. The results led to the proposal that Circinaria gyrosa (Lecanoromycetes, Ascomycota) is one of the most durable astrobiological model lichens. However, although C. gyrosa has been exposed to Mars-like environmental conditions while in a latent state, it has not been exposed in its physiologically active mode. We hypothesize that the astrobiological test system “Circinaria gyrosa,” could be able to be physiologically active and to survive under Mars-like conditions in a simulation chamber, based on previous studies performed at dessicated-dormant stage under simulated Mars-like conditions, that showed a complete recover of the PSII activity (Sánchez et al., 2012). Epifluorescence and confocal laser scanning microscopy (CLSM) showed that living algal cells were more abundant in samples exposed to niche conditions, which simulated the conditions in micro-fissures and micro-caves close to the surface that have limited scattered or time-dependent light exposure, than in samples exposed to full UV radiation. The medulla was not structurally affected, suggesting that the niche exposure conditions did not disturb the lichen thalli structure and morphology as revealed by field emission scanning electron microscopy (FESEM). In addition, changes in the lichen thalli chemical composition were determined by analytical pyrolysis. The chromatograms resulting from analytical pyrolysis at 500°C revealed that lichen samples exposed to niche conditions and full UV radiation consisted primarily of glycosidic compounds, lipids, and sterols, which are typical constituents of the cell walls. However, specific differences could be detected and used as markers of the UV-induced damage to the lichen membranes. Based on its viability responses after rehydration, our study shows that the test lichen survived the 30-day incubation in the Mars chamber particularly under niche conditions. However, the photobiont was not able to photosynthesize under the Mars-like conditions, which indicates that the surface of Mars is not a habitable place for C. gyrosa.
Transmission of vibration from a vibrating plate to the head of standing people

Abstract Little is known about the transmission of vibration to the head when using whole-body vibration (WBV) training machines. This paper investigates the effect of frequency and posture on the transmission of vibration from a vibrating plate to the head of standing people. Nine male participants were exposed to vertical vibration at nine frequencies in the range of 17–46 Hz and vibration acceleration in the range of 7.85–18.64 m/s2 (peak). The participants adopted four standing postures described as standing with locked knee (LK), bent knee (BK), one leg (OL), and one foot to the front and the other to the back (FB). The transmissibility to the head differed among postures (t-test, p < 0.05) and was greatest with the FB posture and smallest with the BK posture. The transmissibility to the head decreased with increasing the frequency (t-test, p < 0.05) but the extent of the decrease depended on the adopted posture. This frequency-posture interaction effect on the transmissibility should be considered when designing a training program. The data will be useful for developing standards/protocols that govern the use of WBV machines as well as for building human body models that can predict potential risks arising from using WBV machines.
A preliminary multifactorial approach describing the relationships among lower extremity alignment, hip muscle activation, and lower extremity joint excursion.

CONTEXT Multiple factors have been suggested to increase the risk of faulty dynamic alignments that predict noncontact anterior cruciate ligament injury. Few researchers have examined this relationship using an integrated, multifactorial approach. OBJECTIVE To describe the relationship among static lower extremity alignment (LEA), hip muscle activation, and hip and knee motion during a single-leg squat. DESIGN Descriptive laboratory study. SETTING Research laboratory. PATIENTS OR OTHER PARTICIPANTS Thirty men (age= 23.9± 3.6 years, height =178.5± 9.9 cm, mass= 82.0± 14.1 kg) and 30 women (age= 22.2± 2.6 years, height= 162.4± 6.3 cm, mass= 60.3± 8.1 kg). MAIN OUTCOME MEASURE(S) Pelvic angle, femoral anteversion, quadriceps angle, tibiofemoral angle, and genu recurvatum were measured to the nearest degree; navicular drop was measured to the nearest millimeter. The average root mean square amplitude of the gluteus medius and maximus muscles was assessed during the single-leg squat and normalized to the peak root mean square value during maximal contractions for each muscle. Kinematic data of hip and knee were also assessed during the single-leg squat. Structural equation modeling was used to describe the relationships among static LEA, hip muscle activation, and joint kinematics, while also accounting for an individual's sex and hip strength. RESULTS Smaller pelvic angle and greater femoral anteversion, tibiofemoral angle, and navicular drop predicted greater hip internal-rotation excursion and knee external-rotation excursion. Decreased gluteus maximus activation predicted greater hip internal-rotation excursion but decreased knee valgus excursion. No LEA characteristic predicted gluteus medius or gluteus maximus muscle activation during the single-leg squat. CONCLUSIONS Static LEA, characterized by a more internally rotated hip and valgus knee alignment and less gluteus maximus activation, was related to commonly observed components of functional valgus collapse during the single-leg squat. This exploratory analysis suggests that LEA does not influence hip muscle activation in controlling joint motion during a single-leg squat.
First detection of dengue virus in the saliva of immunocompetent murine model

The lack of an experimental animal model for the study of dengue pathogenesis is a limiting factor for the development of vaccines and drugs. In previous studies, our group demonstrated the susceptibility of BALB/c mice to infection by dengue virus (DENV) 1 and 2, and the virus was successfully isolated in several organs. In this study, BALB/c mice were experimentally infected intravenously with DENV-4, and samples of their saliva were collected. Viral RNA extracted from the saliva samples was subjected to qRT-PCR, with a detection limit of 0.002 PFU/mL. The presence of DENV-4 viral RNA was detected in the saliva of two mice, presenting viral titers of 109 RNA/mL. The detection of DENV RNA via saliva sampling is not a common practice in dengue diagnosis, due to the lower detection rates in human patients. However, the results observed in this study seem to indicate that, as in humans, detection rates of DENV RNA in mouse saliva are also low, correlating the infection in both cases. This study reports the first DENV detection in the saliva of BALB/c immunocompetent mice experimentally infected with non-neuroadapted DENV-4.
Ocular surface squamous neoplasia in HIV-infected patients: current perspectives

Ocular surface squamous neoplasia (OSSN) refers to a spectrum of conjunctival and corneal epithelial tumors including dysplasia, carcinoma in situ, and invasive carcinoma. In this article, we discuss the current perspectives of OSSN associated with HIV infection, focusing mainly on the epidemiology, pathophysiology, clinical manifestations, diagnosis, and treatment of these tumors in patients with HIV. Upsurge in the incidence of OSSN with the HIV pandemic most severely affected sub-Saharan Africa, due to associated risk factors, such as human papilloma virus and solar ultraviolet exposure. OSSN has been reported as the first presenting sign of HIV/AIDS in 26%–86% cases, and seropositivity is noted in 38%–92% OSSN patients. Mean age at presentation of OSSN has dropped to the third to fourth decade in HIV-positive patients in developing countries. HIV-infected patients reveal large aggressive tumors, higher-grade malignancy, higher incidence of corneal, scleral, and orbital invasion, advanced-stage T4 tumors, higher need for extended enucleation/exenteration, and increased risk of tumor recurrence. Current management of OSSN in HIV-positive individuals is based on standard treatment guidelines described for OSSN in the general population, as there is little information available about various treatment modalities or their outcomes in patients with HIV. OSSN can occur at any time in the disease course of HIV/AIDS, and no significant trend has been discovered between CD4 count and grade of OSSN. Furthermore, the effect of highly active antiretroviral therapy on OSSN is controversial. The current recommendation is to conduct HIV screening in all cases presenting with OSSN to rule out undiagnosed HIV infection. Patient counseling is crucial, with emphasis on regular follow-up to address high recurrence rates and early presentation to an ophthalmologist for of any symptoms in the unaffected eye. Effective evidence-based interventions are needed to allow early diagnosis and treatment, as well as prevention of the disease.
The Influence of Mentoring on the Peer Relationships of Foster Youth in Relative and Nonrelative Care

The influence of a mentoring program (Big Brothers-Big Sisters) on the peer relationships of foster youth in relative and nonrelative care was examined. Youth were randomly assigned to either the treatment or control condition, and changes in their peer relationships were assessed after 18 months. Foster parents were more likely than nonfoster parents to report that their child showed improved social skills, as well as greater comfort and trust interacting with others, as a result of the intervention. In addition, whereas the peer relationships of all nonfoster youth (N = 90) remained stable, treatment foster youth (N = 90) reported improvements in prosocial and self-esteem enhancing support, and control foster youth showed decrements over time. When the foster youth were differentiated further on the basis of their placement, a pattern of findings emerged in which treatment youth in relative foster care reported slight improvements in prosocial support, whereas treatment youth in nonrelative foster care .
Disentangling top-down vs. bottom-up and low-level vs. high-level influences on eye movements over time

Bottom-up and top-down, as well as low-level and high-level factors influence where we fixate when viewing natural scenes. However, the importance of each of these factors and how they interact remains a matter of debate. Here, we disentangle these factors by analysing their influence over time. For this purpose we develop a saliency model which is based on the internal representation of a recent early spatial vision model to measure the low-level bottom-up factor. To measure the influence of high-level bottom-up features, we use a recent DNN-based saliency model. To account for top-down influences, we evaluate the models on two large datasets with different tasks: first, a memorisation task and, second, a search task. Our results lend support to a separation of visual scene exploration into three phases: The first saccade, an initial guided exploration characterised by a gradual broadening of the fixation density, and an steady state which is reached after roughly 10 fixations. Saccade target selection during the initial exploration and in the steady state are related to similar areas of interest, which are better predicted when including high-level features. In the search dataset, fixation locations are determined predominantly by top-down processes. In contrast, the first fixation follows a different fixation density and contains a strong central fixation bias. Nonetheless, first fixations are guided strongly by image properties and as early as 200 ms after image onset, fixations are better predicted by high-level information. We conclude that any low-level bottom-up factors are mainly limited to the generation of the first saccade. All saccades are better explained when high-level features are considered, and later this high-level bottom-up control can be overruled by top-down influences.
An open phase I study assessing the feasibility of the triple combination: oxaliplatin plus irinotecan plus leucovorin/ 5-fluorouracil every 2 weeks in patients with advanced solid tumors.

BACKGROUND The aim of this study was to determine the maximum-tolerated dose (MTD) and the recommended dose of irinotecan and oxaliplatin with a fixed 5-fluorouracil (5-FU)/leucovorin (LV) regimen in patients with metastatic solid tumors. PATIENTS AND METHODS The trial was designed to evaluate escalating doses of oxaliplatin and irinotecan, starting at 60 mg/m2 and 90 mg/m2, respectively, given at day 1 with the full-dose LV5FU2 regimen, given on days 1 and 2 as follows: folinic acid 200 mg/m2 followed by 5-FU 400 mg/m2 bolus and 600 mg/m2 22 h continuous infusion, every 2 weeks. The second cohort of patients was treated at the recommended dose for oxaliplatin and irinotecan with the simplified LV5FU regimen: on day 1, a 2-h infusion of folinic acid (400 mg/m2), followed by a 10-min intravenous bolus of 5-FU (400 mg/m2), followed by a continuous infusion of 5-FU (2400 mg/m2) over 46 h. RESULTS Thirty-four patients were treated at the following dose levels (oxaliplatin/irinotecan mg/m2): 60/90, 60/120, 85/120, 85/150, 85/180, 85/200 and 85/220 and seven patients were treated at the recommended dose with the simplified LV5FU scheme. The MTD was reached at dose level 85/220 mg/m2 but the recommended dose chosen for the second step was 85/180 mg/m2 to keep a better compliance with the biweekly schedule. Main grade 3/4 toxicities per patient included the following: neutropenia in 78% (febrile episodes in 12%), diarrhea in 27%, nausea/vomiting in 24% and peripheral neuropathy in 37% (Lévi's scale). Antitumor activity was observed at almost all dose levels. Most objective responses were observed in digestive malignancies, since 10 out of 11 were obtained in five colorectal cancers, two pancreatic cancers, two cholangiocarcinoma and one gastric cancer. CONCLUSION The recommended dose for the triple association is 85/180 mg/m2 of oxaliplatin and irinotecan, respectively, with LV5FU2 or simplified LV5FU. The antitumor activity in gastrointestinal malignancies should be evaluated in phase II studies in different tumor types.
Identification of Bacterial Protein O-Oligosaccharyltransferases and Their Glycoprotein Substrates

O-glycosylation of proteins in Neisseria meningitidis is catalyzed by PglL, which belongs to a protein family including WaaL O-antigen ligases. We developed two hidden Markov models that identify 31 novel candidate PglL homologs in diverse bacterial species, and describe several conserved sequence and structural features. Most of these genes are adjacent to possible novel target proteins for glycosylation. We show that in the general glycosylation system of N. meningitidis, efficient glycosylation of additional protein substrates requires local structural similarity to the pilin acceptor site. For some Neisserial PglL substrates identified by sensitive analytical approaches, only a small fraction of the total protein pool is modified in the native organism, whereas others are completely glycosylated. Our results show that bacterial protein O-glycosylation is common, and that substrate selection in the general Neisserial system is dominated by recognition of structural homology.
Impact of slow-light enhancement on optical propagation in active semiconductor photonic-crystal waveguides

We derive and validate a set of coupled Bloch wave equations for analyzing the reflection and transmission properties of active semiconductor photonic-crystal waveguides. In such devices, slow-light propagation can be used to enhance the material gain per unit length, enabling, for example, the realization of short optical amplifiers compatible with photonic integration. The coupled-wave analysis is compared to numerical approaches based on the Fourier modal method and a frequency domain finite-element technique. The presence of material gain leads to the buildup of a backscattered field, which is interpreted as distributed feedback effects or reflection at passive-active interfaces, depending on the approach taken. For very large material gain values, the band structure of the waveguide is perturbed, and deviations from the simple coupled Bloch wave model are found.
Deep Latent Dirichlet Allocation with Topic-Layer-Adaptive Stochastic Gradient Riemannian MCMC

It is challenging to develop stochastic gradient based scalable inference for deep discrete latent variable models (LVMs), due to the difficulties in not only computing the gradients, but also adapting the step sizes to different latent factors and hidden layers. For the Poisson gamma belief network (PGBN), a recently proposed deep discrete LVM, we derive an alternative representation that is referred to as deep latent Dirichlet allocation (DLDA). Exploiting data augmentation and marginalization techniques, we derive a block-diagonal Fisher information matrix and its inverse for the simplex-constrained global model parameters of DLDA. Exploiting that Fisher information matrix with stochastic gradient MCMC, we present topic-layer-adaptive stochastic gradient Riemannian (TLASGR) MCMC that jointly learns simplex-constrained global parameters across all layers and topics, with topic and layer specific learning rates. State-of-the-art results are demonstrated on big data sets.
Associations between Acute and Chronic Effects of Exercise on Indicators of Metabolic Health: A Pilot Training Trial

Background The interindividual variability in the health-related efficacy of regular endurance training is high. This impedes on the individual optimization of preventive training prescriptions when optimal efficacy is intended. As a consequence, health-gains remain below what could be achieved. Practicable predictors of an individual’s responsiveness to physical exercise would offer a solution to this problem. Therefore, the present study aims to test the association of acute changes in indicators of metabolic health after an exhaustive exercise test and the respective chronic changes in response to an endurance training program. Methods Fasting blood samples of healthy, untrained, non-smoking subjects (n=12, age 49 ± 7 years; body mass index 29 ± 4; maximum oxygen uptake 34 ± 7 ml·min-1·kg-1) were collected before and 1 hour after an exhaustive exercise test as well as after a 4 week supervised training period (walking / running 4 times per week at 60 % heart rate reserve). Results A close linear relationship between acute and chronic changes could be demonstrated for insulin concentration (p=0.001; r=0.83), the fasting indicator of insulin sensitivity HOMA-IR (p<0.001; r=0.78) and non-esterified fatty acid concentration (p=0.001; r=0.88). No association became apparent for standard blood lipid parameters. Conclusion It is concluded that the magnitude of acute exercise-induced changes in indicators of insulin sensitivity and non-esterified fatty acid concentration is a promising candidate for the prediction of chronic training induced changes in the respective parameter. However, further studies are needed to assess predictive accuracy. Trial Registration www.clinicaltrials. gov NCT00934206 http://www.clinicaltrials. gov/ct2/show/NCT00934206
Exploring Data Augmentation for Improved Singing Voice Detection with Neural Networks

In computer vision, state-of-the-art object recognition systems rely on label-preserving image transformations such as scaling and rotation to augment the training datasets. The additional training examples help the system to learn invariances that are difficult to build into the model, and improve generalization to unseen data. To the best of our knowledge, this approach has not been systematically explored for music signals. Using the problem of singing voice detection with neural networks as an example, we apply a range of label-preserving audio transformations to assess their utility for music data augmentation. In line with recent research in speech recognition, we find pitch shifting to be the most helpful augmentation method. Combined with time stretching and random frequency filtering, we achieve a reduction in classification error between 10 and 30%, reaching the state of the art on two public datasets. We expect that audio data augmentation would yield significant gains for several other sequence labelling and event detection tasks in music information retrieval.
Donor pulmonary intravascular nonclassical monocytes recruit recipient neutrophils and mediate primary lung allograft dysfunction

Donor nonclassical monocytes mediate primary lung allograft dysfunction by recruiting neutrophils via MyD88-dependent production of CXCL2. Nonclassical monocytes prompt primary graft dysfunction Despite concerted efforts, primary graft dysfunction is a major cause of graft failure after organ transplantation. In lung transplantation, primary graft dysfunction is known to be mediated by early neutrophil infiltration. Zheng et al. used syngeneic and allogeneic mouse models of lung transplantation to show that nonclassical monocytes were the key cell population recruiting these destructive neutrophils. These intravascular cells were donor-derived and were also detectable in human lung grafts being used for transplant. Because depletion of nonclassical monocytes prevented primary graft dysfunction in the mouse models, targeting this cell population during human transplant could lead to improved rates of graft success. Primary graft dysfunction is the predominant driver of mortality and graft loss after lung transplantation. Recruitment of neutrophils as a result of ischemia-reperfusion injury is thought to cause primary graft dysfunction; however, the mechanisms that regulate neutrophil influx into the injured lung are incompletely understood. We found that donor-derived intravascular nonclassical monocytes (NCMs) are retained in human and murine donor lungs used in transplantation and can be visualized at sites of endothelial injury after reperfusion. When NCMs in the donor lungs were depleted, either pharmacologically or genetically, neutrophil influx and lung graft injury were attenuated in both allogeneic and syngeneic models. Similar protection was observed when the patrolling function of donor NCMs was impaired by deletion of the fractalkine receptor CX3CR1. Unbiased transcriptomic profiling revealed up-regulation of MyD88 pathway genes and a key neutrophil chemoattractant, CXCL2, in donor-derived NCMs after reperfusion. Reconstitution of NCM-depleted donor lungs with wild-type but not MyD88-deficient NCMs rescued neutrophil migration. Donor NCMs, through MyD88 signaling, were responsible for CXCL2 production in the allograft and neutralization of CXCL2 attenuated neutrophil influx. These findings suggest that therapies to deplete or inhibit NCMs in donor lung might ameliorate primary graft dysfunction with minimal toxicity to the recipient.