Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid categorization of natural face images in the infant right hemisphere

Human performance at categorizing natural visual images surpasses automatic algorithms, but how and when this function arises and develops remain unanswered. We recorded scalp electrical brain activity in 4–6 months infants viewing images of objects in their natural background at a rapid rate of 6 images/second (6 Hz). Widely variable face images appearing every 5 stimuli generate an electrophysiological response over the right hemisphere exactly at 1.2 Hz (6 Hz/5). This face-selective response is absent for phase-scrambled images and therefore not due to low-level information. These findings indicate that right lateralized face-selective processes emerge well before reading acquisition in the infant brain, which can perform figure-ground segregation and generalize face-selective responses across changes in size, viewpoint, illumination as well as expression, age and gender. These observations made with a highly sensitive and objective approach open an avenue for clarifying the developmental course of natural image categorization in the human brain. DOI: http://dx.doi. org/10.7554/eLife.06564. 001
Benefit–risk assessment of new and emerging treatments for hepatitis C: focus on simeprevir and sofosbuvir

: Greater understanding of the hepatitis C virus (HCV) genome and life cycle of the HCV virion allows for new targets for therapy that directly act on the viral machinery to inhibit replication. Numerous direct-acting antivirals are in development, and four have been brought to market. Simeprevir, a second-generation protease inhibitor, has been approved for HCV genotype 1 patients in combination with pegylated interferon- α and ribavirin. Sofosbuvir, a novel nucleotide analog, has pangenotypic coverage and has been approved for HCV genotype 1 patients with ribavirin and pegylated interferon- α . For HCV genotypes 2 and 3, an all-oral regimen of sofosbuvir with ribavirin has become the new gold standard for treatment. The efficacy and safety for these two novel therapies among various subpopulations of those infected with chronic hepatitis C are discussed in the following review. In addition, off-label and future therapeutic regimens are addressed, as well as the concerns about cost of current and future therapies.
Circulating miRNAs as biomarkers for oral squamous cell carcinoma recurrence in operated patients

MicroRNAs (miRNAs) are small regulatory non-coding RNAs for which altered expression in cancers can serve as potential biomarkers for diseases. We here investigated whether circulating miRNAs can serve as biomarkers for predicting post-operational recurrence of oral squamous cell carcinoma (OSCC) in patients. Plasma samples from 8 Danish OSCC patients were collected before, and one year after surgical operation, as well as from 3 Danish healthy controls and subjected to miRNA profiling by next generation sequencing. Disease recurrence did not occur in the 8 patients when the post-operative plasma samples were collected. Based on the sequencing data, three up-regulated miRNAs (miR-148a-3p, miR-26a-5p and miR-21-5p) and three down-regulated miRNAs (miR-375, miR-92b-3p and miR-486-5p) in the OSCC samples compared to healthy controls were selected for qRT-PCR validation in a Chinese cohort of 20 plasma samples collected before, and 9-12 months after surgical operation, and 18 healthy controls. Disease recurrence had occurred in 8 out of the 20 Chinese patients at the time their post-operative plasma samples were collected. The results of qRT-PCR showed that down-regulation of miR-486-5p, miR-375 and miR-92b-3p were highly associated with OSCC recurrence. This study indicates that the plasma miRNA profile is altered in OSCC during its progression and can be used to monitor the likelihood of OSCC recurrence in patients after surgery.
New strategy to improve estimation of diffuse attenuation coefficient for highly turbid inland waters

The diffuse attenuation coefficient, Kd(λ), is an important water optical property. Detection of Kd(λ) by means of remote sensing can provide significant assistance in understanding water environment conditions and many biogeochemical processes. Even when existing algorithms exhibit good performance in clear open ocean and turbid coastal waters, accurate quantification of highly turbid inland water bodies can still be a challenge due to their bio-optical complexity. In this study, we examined the performance of two typical pre-existing Kd(490) models in inland water bodies from Lake Taihu, Lake Chaohu, and the Three Gorges Reservoir in China. On the basis of water optical classification, new Kd(490) models were developed for these waters by means of the support vector machine approach. The obtained results showed that the two pre-existing Kd(490) models presented relatively large errors by comparison with the new models, with mean absolute percentage error (MAPE) values above ~30%. More importantly, among the new models, type-specific models generally outperformed the aggregated model. For water classified as Type 1 + Type 2, the type-specific model produced validation errors with MAPE = 16.8% and RMSE = 0.98 m−1. For water classified as Type 3, the MAPE and RMSE of the type-specific model were found to be 18.8% and 1.85 m−1, respectively. The findings in this study demonstrate that water classification (prior to algorithm development) is needed for the development of excellent Kd(490) retrieval algorithms, and the type-specific models thus developed are an important supplement to existing Kd(490) retrieval models for highly turbid inland waters.
Transduction of Signals during Somatic Embryogenesis

Somatic embryogenesis (SE) is an in vitro biological process in which bipolar structures (somatic embryos) can be induced to form from somatic cells and regenerate into whole plants. Acquisition of the embryogenic potential in culture is initiated when some competent cells within the explants respond to inductive signals (mostly plant growth regulators, PRGs), and de-differentiate into embryogenic cells. Such cells, “canalized” into the embryogenic developmental pathway, are able to generate embryos comparable in structure and physiology to their in vivo counterparts. Genomic and transcriptomic studies have identified several pathways governing the initial stages of the embryogenic process. In this review, the authors emphasize the importance of the developmental signals required for the progression of embryo development, starting with the de-differentiation of somatic cells and culminating with tissue patterning during the formation of the embryo body. The action and interaction of PGRs are highlighted, along with the participation of master regulators, mostly transcription factors (TFs), and proteins involved in stress responses and the signal transduction required for the initiation of the embryogenic process.
GSK3 and Alzheimer’s Disease: Facts and Fiction…

The physiological functions and pathological roles of the Glycogen synthase kinase-type 3 (GSK3) kinases in peripheral and central systems are diverse and complex, and therefore hard to unravel in molecular detail in vivo. Our assignment to review and discuss available data to clarify the actual position of these kinases in the pathology of Alzheimer’s dementia (AD) was both ambitious and easy. On the one hand, numerous studies are available in isolated, recombinant, or cell-based systems, which have resulted in very diverse data-sets that are hardly informative for the brain in vivo. At the other extreme, reliable, and relevant models for the role of GSK3 in CNS are rare, if not lacking. Moreover, (too) many in vivo studies used Li+ as “specific” inhibitor of GSK3, which is factually not valid because lithium ions are neither specific nor potent inhibitors of GSK3 in vivo. More specific pharmacological inhibitors of GSK3 have met with considerable problems, and are reviewed by others in this issue or elsewhere. We concentrate here on AD-related aspects of GSK3 in brain in vivo, mainly studied in transgenic mice and highlight some of the more important issues, among many remaining: activation of GSK3 by amyloid, phosphorylation of protein tau, effects on or interference with synaptic activity, differentiation between both GSK3 isoforms. These relate directly to brain function, and brain dysfunction in AD, and are to be resolved if we want to understand the molecular pathology of this dreadful disease.
Modeling the Molecular Impact of SARS-CoV-2 Infection on the Renin-Angiotensin System

SARS-CoV-2 infection is mediated by the binding of its spike protein to the angiotensin-converting enzyme 2 (ACE2), which plays a pivotal role in the renin-angiotensin system (RAS). The study of RAS dysregulation due to SARS-CoV-2 infection is fundamentally important for a better understanding of the pathogenic mechanisms and risk factors associated with COVID-19 coronavirus disease and to design effective therapeutic strategies. In this context, we developed a mathematical model of RAS based on data regarding protein and peptide concentrations; the model was tested on clinical data from healthy normotensive and hypertensive individuals. We used our model to analyze the impact of SARS-CoV-2 infection on RAS, which we modeled through a downregulation of ACE2 as a function of viral load. We also used it to predict the effect of RAS-targeting drugs, such as RAS-blockers, human recombinant ACE2, and angiotensin 1–7 peptide, on COVID-19 patients; the model predicted an improvement of the clinical outcome for some drugs and a worsening for others. Our model and its predictions constitute a valuable framework for in silico testing of hypotheses about the COVID-19 pathogenic mechanisms and the effect of drugs aiming to restore RAS functionality.
The occurrence and chemical implications of geothermal convection of seawater in continental shelves

Geothermal convection is an important driving force for fluid flow and diagenesis in carbonate platforms, and the similar shape of continental shelves in general suggests that geothermal convection could occur in continental shelves around the world. Numerical models based on seven transects of the shelf off the east coast of North America were developed to bracket possible fluxes. Simulations assuming relatively permeable sediments (medium‐grained carbonates) failed to produce significant thermal variations, suggesting that chemical tracers will be required to detect this flow in the field. Fluxes calculated assuming lower permeabilities (fine grained carbonates) between Cape Fear and the Savannah River were approximately 3 orders of magnitude smaller than river discharge for the area, a difference similar to that between global river discharge and hydrothermal convection at mid‐ocean ridges. Sediment diagenesis during geothermal convection in continental shelves thus has the potential to affect ocean chemical budgets, including potassium, calcium, and magnesium.
Subglacial erosion forms in northwest Ireland

Subglacial erosional forms are commonly found on bedrock substrates inside the Late Weichselian ice margin in County Donegal, northwest Ireland, and can be used to provide detailed information on subglacial processes and environments. The erosional forms occur on spatial scales from whalebacks (tens of metres in scale), to asymmetric and channelized bedrock‐cut scours (tens of cm in scale) and striations (mm scale). Processes responsible for development of subglacial erosional forms occur along a continuum, from free meltwater existing as a laterally extensive sheet at the ice‐bed interface, to abrasion by basal ice. Channelized bedrock‐cut scours are particularly common in County Donegal, and show asymmetric and meandering thalwegs, U‐shaped cross‐profiles and steep lateral margins. Innermost parts of the scours are highly polished and have striations that follow thalweg direction. In places, bedrock surfaces are overlain by a delicate polish and thin calcite cement, and are buried beneath glacial till. Based on their morphology, the bedrock scours are interpreted as s‐forms caused by high‐pressure subglacial meltwater erosion. Striations within the scoured channels reflect periods of ice‐bed coupling and subglacial abrasion. The range of features observed here was used to consider relationships between subglacial topography, hydraulic processes and ice‐bed coupling. Precipitation of calcite cement took place in depressions on the bedrock surface by CO2 degassing. Infilling of depressions by glacial till formed a new type of ‘sticky spot’ related to spatial variations in subglacial water pressure. The temporal evolution of sticky spots reflects interactions within the subglacial environment between subglacial relief, hydraulic regime and ice‐bed coupling.
Artificial Neural Networks for the Diagnosis of Aggressive Periodontitis Trained by Immunologic Parameters

There is neither a single clinical, microbiological, histopathological or genetic test, nor combinations of them, to discriminate aggressive periodontitis (AgP) from chronic periodontitis (CP) patients. We aimed to estimate probability density functions of clinical and immunologic datasets derived from periodontitis patients and construct artificial neural networks (ANNs) to correctly classify patients into AgP or CP class. The fit of probability distributions on the datasets was tested by the Akaike information criterion (AIC). ANNs were trained by cross entropy (CE) values estimated between probabilities of showing certain levels of immunologic parameters and a reference mode probability proposed by kernel density estimation (KDE). The weight decay regularization parameter of the ANNs was determined by 10-fold cross-validation. Possible evidence for 2 clusters of patients on cross-sectional and longitudinal bone loss measurements were revealed by KDE. Two to 7 clusters were shown on datasets of CD4/CD8 ratio, CD3, monocyte, eosinophil, neutrophil and lymphocyte counts, IL-1, IL-2, IL-4, INF-γ and TNF-α level from monocytes, antibody levels against A. actinomycetemcomitans (A.a.) and P.gingivalis (P.g.). ANNs gave 90%–98% accuracy in classifying patients into either AgP or CP. The best overall prediction was given by an ANN with CE of monocyte, eosinophil, neutrophil counts and CD4/CD8 ratio as inputs. ANNs can be powerful in classifying periodontitis patients into AgP or CP, when fed by CE values based on KDE. Therefore ANNs can be employed for accurate diagnosis of AgP or CP by using relatively simple and conveniently obtained parameters, like leukocyte counts in peripheral blood. This will allow clinicians to better adapt specific treatment protocols for their AgP and CP patients.
The ascendance of Israel's radical right

The Israeli people were stunned in 1984 when they learned of a barely averted plot to blow up five buses full of Arab passengers and an earlier attempt to blow up the Dome of the Rock, the holy Muslim mosque in Jerusalem. Even more shocking was the discovery that the terrorists in question were not a bizarre radical sect, but members of the Gush Emunim, "the Block of the Faithful," a fundamentalist group committed to establishing Jewish settlements in the West Bank. For the first time, Israelis had to confront the fact that the rise of the Radical Right--and the religious fundamentalism, extreme nationalism, and aggressive anti-Arab sentiment associated with it--was becoming a significant part of the nation's public life. The first book to examine the origins, convictions, and political impact of the entire Radical Right, The Ascendance of Israel's Radical Right provides extraordinary insights into a political camp whose influence pervades Israeli politics and culture as well as Arab-Israeli relations. Sprinzak traces the Zionist roots of the Radical Right and its reemergence following the Six-Day War and the Camp David accords. He examines the increasing control of the Radical Right over the settlements in the West Bank, its penetration of more moderate parties such as Likud and the National Religious Party, and its reaction to the Intafada and the Persian Gulf Crisis. With in-depth portraits of the major movements--including the Tehiya, Tzomet, and Moledet parties, Gush Emunim, and the late Meir Kahane and his Kach party, and various underground or terrorist groups--he sheds new light on the people and events which produce such intense fervor and on their political beliefs--for instance, the views that Arabs should be "transferred" from the occupied territories and that Israel was founded to establish a safe home for the Jews, not to protect the human rights of the Palestinians. Sprinzak argues that approximately 20 to 25 percent of Israeli citizens share the convictions of the Radical Right, and that it is especially strong among the young. Indeed, as the message of this camp spreads throughout the country, Sprinzak predicts that the Radical Right's impact on Israeli politics and national security will only increase. As The Ascendance of Israel's Radical Right shows, the Radical Right is not--as is often thought--a small lunatic fringe, but a major school of Israeli Zionism, whose ideas are propagated by sophisticated and thoughtful leaders with large public appeal. Understanding what the Radical Right has already achieved, and how it is currently shaping much of Israel's government agenda is important for every Israeli and Arab, as well as anyone who is concerned with the future of the Middle East.
High concentrations of Na+ and Cl– ions in soil solution have simultaneous detrimental effects on growth of faba bean under salinity stress

Despite the fact that most plants accumulate both sodium (Na+) and chloride (Cl–) ions to high concentration in their shoot tissues when grown in saline soils, most research on salt tolerance in annual plants has focused on the toxic effects of Na+ accumulation. There have also been some recent concerns about the ability of hydroponic systems to predict the responses of plants to salinity in soil. To address these two issues, an experiment was conducted to compare the responses to Na+ and to Cl– separately in comparison with the response to NaCl in a soil-based system using two varieties of faba bean (Vicia faba), that differed in salinity tolerance. The variety Nura is a salt-sensitive variety that accumulates Na+ and Cl– to high concentrations while the line 1487/7 is salt tolerant which accumulates lower concentrations of Na+ and Cl–. Soils were prepared which were treated with Na+ or Cl– by using a combination of different Na+ salts and Cl– salts, respectively, or with NaCl. While this method produced Na+-dominant and Cl–-dominant soils, it unavoidably led to changes in the availability of other anions and cations, but tissue analysis of the plants did not indicate any nutritional deficiencies or toxicities other than those targeted by the salt treatments. The growth, water use, ionic composition, photosynthesis, and chlorophyll fluorescence were measured. Both high Na+ and high Cl– reduced growth of faba bean but plants were more sensitive to Cl– than to Na+. The reductions in growth and photosynthesis were greater under NaCl stress and the effect was mainly additive. An important difference to previous hydroponic studies was that increasing the concentrations of NaCl in the soil increased the concentration of Cl– more than the concentration of Na+. The data showed that salinity caused by high concentrations of NaCl can reduce growth by the accumulation of high concentrations of both Na+ and Cl– simultaneously, but the effects of the two ions may differ. High Cl– concentration reduces the photosynthetic capacity and quantum yield due to chlorophyll degradation which may result from a structural impact of high Cl– concentration on PSII. High Na+ interferes with K+ and Ca2+ nutrition and disturbs efficient stomatal regulation which results in a depression of photosynthesis and growth. These results suggest that the importance of Cl– toxicity as a cause of reductions in growth and yield under salinity stress may have been underestimated.
Entrainment of Nitrate in the Fraser River Estuary and its Biological Implications. III. Effects of Winds

Abstract Two 24-h time series of vertical profiles of velocity, salinity, temperature, fluorescence and NO 3 were conducted during weak and strong winds (2·2 and 7·3 m s −1 , respectively) to demonstrate wind effects on entrainment of NO 3 near the mouth of the Fraser River. The results showed that wind-induced entrainment of NO 3 was mainly responsible for the increased NO 3 concentrations in the upper layer because shear velocities between the upper and lower layers were great enough to break down the pycnocline and allow diapycnal mixing to occur. Strong shear was indicated by Richardson numbers less than 0·25 near the depth at which flows in the upper and lower layers moved opposite to each other. As a result of wind-induced entrainment and mixing, the NO 3 minimum in the water column was gradually eroded and disappeared at the end of the time series during the strong wind event. The amount of entrained NO 3 under windy conditions (44 mmol m −2 ) was almost three times that (16 mmol m −2 ) under weak winds. The high ratios of the amount of entrained NO 3 to river-borne NO 3 (12 under windy conditions and 5·6 under weak winds) indicates that wind-induced entrainment of NO 3 in summer is particularly important for new production. Because turbulent energy came from winds, mixing started at the surface and moved downward. Thus, phytoplankton cells remained in the surface mixed layer, and responded to the entrained nutrients and grew rapidly. Phytoplankton biomass and primary production in the water column increased at the end of the time series, compared to the beginning.
Network Scaling Effects in Graph Analytic Studies of Human Resting-State fMRI Data

Graph analysis has become an increasingly popular tool for characterizing topological properties of brain connectivity networks. Within this approach, the brain is modeled as a graph comprising N nodes connected by M edges. In functional magnetic resonance imaging (fMRI) studies, the nodes typically represent brain regions and the edges some measure of interaction between them. These nodes are commonly defined using a variety of regional parcellation templates, which can vary both in the volume sampled by each region, and the number of regions parcellated. Here, we sought to investigate how such variations in parcellation templates affect key graph analytic measures of functional brain organization using resting-state fMRI in 30 healthy volunteers. Seven different parcellation resolutions (84, 91, 230, 438, 890, 1314, and 4320 regions) were investigated. We found that gross inferences regarding network topology, such as whether the brain is small-world or scale-free, were robust to the template used, but that both absolute values of, and individual differences in, specific parameters such as path length, clustering, small-worldness, and degree distribution descriptors varied considerably across the resolutions studied. These findings underscore the need to consider the effect that a specific parcellation approach has on graph analytic findings in human fMRI studies, and indicate that results obtained using different templates may not be directly comparable.