Miracle-dz/UniFAR-FTUs huggingface dataset:
Beyond the Medial Regions of Prefrontal Cortex in the Regulation of Fear and Anxiety

Fear and anxiety are adaptive responses but if left unregulated, or inappropriately regulated, they become biologically and socially maladaptive. Dysregulated emotions are manifest in a wide variety of psychiatric and neurological conditions but the external expression gives little indication of the underlying causes, which are inevitably multi-determined. To go beyond the overt phenotype and begin to understand the causal mechanisms leading to conditions characterized by anxiety and disorders of mood, it is necessary to identify the base psychological processes that have become dysregulated, and map them on to their associated neural substrates. So far, attention has been focused primarily on the medial regions of prefrontal cortex (PFC) and in particular their contribution to the expression and extinction of conditioned fear. However, functional neuroimaging studies have shown that the sphere of influence within the PFC is not restricted to its medial regions, but extends into dorsal, ventrolateral (vlPFC) and orbitofrontal (OFC) regions too; although the causal role of these other areas in the regulation of fear and anxiety remains to be determined and in the case of the OFC, existing findings are conflicting. Here, we review the evidence for the contribution of these other regions in negative emotion regulation in rodents and old world and new world monkeys. We consider a variety of different contexts, including conditioned and innate fear, learned and unlearned anxiety and cost-benefit decision-making, and a range of physiological and behavioral measures of emotion. It is proposed that both the OFC and vlPFC contribute to emotion regulation via their involvement, respectively, in the prediction of future outcomes and higher-order attentional control. The fractionation of these neurocognitive and neurobehavioral systems that regulate fear and anxiety opens up new opportunities for diagnostic stratification and personalized treatment strategies.
Genome-Wide Binding Map of the HIV-1 Tat Protein to the Human Genome

The HIV-1 Trans-Activator of Transcription (Tat) protein binds to multiple host cellular factors and greatly enhances the level of transcription of the HIV genome. While Tat's control of viral transcription is well-studied, much less is known about the interaction of Tat with the human genome. Here, we report the genome-wide binding map of Tat to the human genome in Jurkat T cells using chromatin immunoprecipitation combined with next-generation sequencing. Surprisingly, we found that ∼53% of the Tat target regions are within DNA repeat elements, greater than half of which are Alu sequences. The remaining target regions are located in introns and distal intergenic regions; only ∼7% of Tat-bound regions are near transcription start sites (TSS) at gene promoters. Interestingly, Tat binds to promoters of genes that, in Jurkat cells, are bound by the ETS1 transcription factor, the CBP histone acetyltransferase and/or are enriched for histone H3 lysine 4 tri-methylation (H3K4me3) and H3K27me3. Tat binding is associated with genes enriched with functions in T cell biology and immune response. Our data reveal that Tat's interaction with the host genome is more extensive than previously thought, with potentially important implications for the viral life cycle.
SVDNet for Pedestrian Retrieval

This paper proposes the SVDNet for retrieval problems, with focus on the application of person re-identification (reID). We view each weight vector within a fully connected (FC) layer in a convolutional neuron network (CNN) as a projection basis. It is observed that the weight vectors are usually highly correlated. This problem leads to correlations among entries of the FC descriptor, and compromises the retrieval performance based on the Euclidean distance. To address the problem, this paper proposes to optimize the deep representation learning process with Singular Vector Decomposition (SVD). Specifically, with the restraint and relaxation iteration (RRI) training scheme, we are able to iteratively integrate the orthogonality constraint in CNN training, yielding the so-called SVDNet. We conduct experiments on the Market-1501, CUHK03, and DukeMTMC-reID datasets, and show that RRI effectively reduces the correlation among the projection vectors, produces more discriminative FC descriptors, and significantly improves the re-ID accuracy. On the Market-1501 dataset, for instance, rank-1 accuracy is improved from 55.3% to 80.5% for CaffeNet, and from 73.8% to 82.3% for ResNet-50.
Inverse Procedural Modelling of Trees

Procedural tree models have been popular in computer graphics for their ability to generate a variety of output trees from a set of input parameters and to simulate plant interaction with the environment for a realistic placement of trees in virtual scenes. However, defining such models and their parameters is a difficult task. We propose an inverse modelling approach for stochastic trees that takes polygonal tree models as input and estimates the parameters of a procedural model so that it produces trees similar to the input. Our framework is based on a novel parametric model for tree generation and uses Monte Carlo Markov Chains to find the optimal set of parameters. We demonstrate our approach on a variety of input models obtained from different sources, such as interactive modelling systems, reconstructed scans of real trees and developmental models.
A dual epigenomic approach for the search of obesity biomarkers: DNA methylation in relation to diet‐induced weight loss

Epigenetics could help to explain individual differences in weight loss after an energy‐restriction intervention. Here, we identify novel potential epigenetic biomarkers of weight loss, comparing DNA methylation patterns of high and low responders to a hypocaloric diet. Twenty‐five overweight or obese men participated in an 8‐wk caloric restriction intervention. DNA was isolated from peripheral blood mononuclear cells and treated with bisulfite. The basal and endpoint epigenetic differences between high and low responders were analyzed by methylation microarray, which was also useful in comparing epigenetic changes due to the nutrition intervention. Subsequently, MALDI‐TOF mass spectrometry was used to validate several relevant CpGs and the surrounding regions. DNA methylation levels in several CpGs located in the ATP10A and CD44 genes showed statistical baseline differences depending on the weight‐loss outcome. At the treatment endpoint, DNA methylation levels of several CpGs on the WT1 promoter were statistically more methylated in the high than in the low responders. Finally, different CpG sites from WT1 and ATP10A were significantly modified as a result of the intervention. In summary, hypocaloricdiet‐induced weight loss in humans could alter DNA methylation status of specific genes. Moreover, baseline DNA methylation patterns may be used as epigenetic markers that could help to predict weight loss. —Milagro, F. I. , Campion, J., Cordero, P., Goyenechea, E. , Gómez‐Uriz, A. M. , Abete, I. , Zulet, M. A. , Martínez, J. A. A dual epigenomic approach for the search of obesity biomarkers: DNA methylation in relation to diet‐induced weight loss. FASEB J. 25, 1378–1389 (2011). www.fasebj. org
Characterization of BOF Dust for Pellets Production Used in Blast Furnace

In order to minimize the incorrect disposal of dust generated in the basic oxygen furnace (BOF) converter and to generate a new application for this solid residue, a simple characterization route was proposed. The powder residue is used to produce self-reducing pellets and can be used in the blast furnace process. The chemical analysis of the dust was carried out using Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES), and some elements as Fe, Si, P, Al and Ca were detected in high amount, as the iron which achieved about 65% concentration. Moreover, the X-ray diffraction analysis indicated that the iron was found in the phases, mainly, as magnetite (Fe3O4) and hematite (Fe2O3) while quartz (SiO2) and calcite (CaCO3) were the major impurities. The spectrometry dispersive energy (SDE) analysis confirmed the presence of such elements and the images obtained by SEM allowed visualizing the morphology of the particles. The average of particle size distribution of the dust was 0.053 mm which is suitable for self-agglomerates pellets.
Tularemia Outbreak Investigation in Kosovo: Case Control and Environmental Studies

A large outbreak of tularemia occurred in Kosovo in the early postwar period, 1999-2000. Epidemiologic and environmental investigations were conducted to identify sources of infection, modes of transmission, and household risk factors. Case and control status was verified by enzyme-linked immunosorbent assay, Western blot, and microagglutination assay. A total of 327 serologically confirmed cases of tularemia pharyngitis and cervical lymphadenitis were identified in 21 of 29 Kosovo municipalities. Matched analysis of 46 case households and 76 control households suggested that infection was transmitted through contaminated food or water and that the source of infection was rodents. Environmental circumstances in war-torn Kosovo led to epizootic rodent tularemia and its spread to resettled rural populations living under circumstances of substandard housing, hygiene, and sanitation.
From Hybrid Systems to Universal Plans via Domain Compilation

While universal plans tell a system how to reach a goal regardless of what state it is in, such plans can be too large to represent. Hybrid systems execute plans where each action is implemented to robustly produce effects if the world does not stray outside the action's control envelope. This paper presents a middle ground between these two extremes that uses plans, but also enables much larger control envelopes using a real-time planner that finds optimal n step plans to achieve a set of goals if one exists.
Is anxiety associated with hot flashes in women with breast cancer?

ObjectiveWomen with breast cancer are at higher risk for experiencing hot flashes (HFs), which is attributable, in large part, to systemic cancer treatments and their effects on estrogen levels. However, other factors, such as anxiety, could also play a role. This study aimed to assess the cross-sectional and temporal relationships between anxiety and HFs among women treated for breast cancer and to clarify the direction of these relationships. MethodsFifty-six women recently treated for breast cancer were assessed prospectively using a 14-day Hot Flashes and Anxiety Diary (HFAD). Anxiety and HFs were also assessed using the Hospital Anxiety and Depression Scale–anxiety subscale and the Menopause-Specific Quality of Life Questionnaire–vasomotor subscale. In addition, HFs were objectively recorded for a continuous 24-hour period using home-based sternal skin conductance. ResultsNo cross-sectional relationship was found between anxiety and subjectively assessed HFs, or between anxiety and the frequency and intensity of objectively assessed HFs. However, a greater anxiety level on the HFAD was significantly associated with a shorter time to reach the HF peak, as assessed with sternal skin conductance (partial Spearman correlation coefficient rsp = −0.44). Moreover, greater anxiety predicted more severe self-reported HFs on the following night, both assessed with the HFAD (rsp = 0.13). Conversely, self-reported diurnal and nocturnal HFs on the HFAD did not predict next-day anxiety level. ConclusionsThis study reveals a significant relationship between anxiety and faster-developing objectively measured HFs. Furthermore, anxiety has been found to significantly predict subsequent increases in self-reported HFs, suggesting that strategies that target anxiety could potentially have a beneficial effect on HFs in women with breast cancer.
E-2-hexenal promotes susceptibility to Pseudomonas syringae by activating jasmonic acid pathways in Arabidopsis

Green leaf volatiles (GLVs) are C6-molecules – alcohols, aldehydes, and esters – produced by plants upon herbivory or during pathogen infection. Exposure to this blend of volatiles induces defense-related responses in neighboring undamaged plants, thus assigning a role to GLVs in regulating plant defenses. Here we compared Arabidopsis thaliana ecotype Landsberg erecta (Ler) with a hydroperoxide lyase line, hpl1, unable to synthesize GLVs, for susceptibility to Pseudomonas syringae pv. tomato (DC3000). We found that the growth of DC3000 was significantly reduced in the hpl1 mutant. This phenomenon correlated with lower jasmonic acid (JA) levels and higher salicylic acid levels in the hpl1 mutant. Furthermore, upon infection, the JA-responsive genes VSP2 and LEC were only slightly or not induced, respectively, in hpl1. This suggests that the reduced growth of DC3000 in hpl1 plants is due to the constraint of JA-dependent responses. Treatment of hpl1 plants with E-2-hexenal, one of the more reactive GLVs, prior to infection with DC3000, resulted in increased growth of DC3000 in hpl1, thus complementing this mutant. Interestingly, the growth of DC3000 also increased in Ler plants treated with E-2-hexenal. This stronger growth was not dependent on the JA-signaling component MYC2, but on ORA59, an integrator of JA and ethylene signaling pathways, and on the production of coronatine by DC3000. GLVs may have multiple effects on plant–pathogen interactions, in this case reducing resistance to Pseudomonas syringae via JA and ORA59.
Human placenta and chorion: potential additional sources of hematopoietic stem cells for transplantation

BACKGROUND: Hematopoietic stem cell (HSC) transplantation is an essential element of medical therapy, leading to cures of previously incurable hematological and nonhematological diseases. Many patients do not find matched donors in a timely manner, which has driven efforts to find alternative pools of transplantable HSCs. The use of umbilical cord blood (UCB) as a source of transplantable HSCs began more than two decades ago. However, the use of UCB as a reliable source of HSCs for transplantation still faces crucial challenges: the number of HSCs present in a unit of UCB is usually sufficient for younger children but not for adults, and the persistent delayed engraftment often seen can result in high rates of infection and mortality.
Output feedback control design for Takagi-Sugeno fuzzy bilinear time-delay systems

This paper is concerned with stability analysis and output feedback control design of fuzzy bilinear systems with time-varying delay. First, we consider the stability of the closed-loop systems by assuming a special form of a fuzzy controller. A stability condition is given in terms of linear matrix inequality (LMI). Based on such a stability condition, we propose a state feedback stabilizing control design for fuzzy bilinear systems with time-varying delays. Next, we consider a fuzzy observer design for the same class of systems. Then, we show that state feedback stabilizing controller and observer make an output feedback stabilizing controller. Finally, we give some numerical examples to illustrate our design procedures and to show the effectiveness of our approach.
Comparison of VHH-Fc antibody production in Arabidopsis thaliana, Nicotiana benthamiana and Pichia pastoris.

VHHs or nanobodies are widely acknowledged as interesting diagnostic and therapeutic tools. However, for some applications, multivalent antibody formats, such as the dimeric VHH-Fc format, are desired to increase the functional affinity. The scope of this study was to compare transient expression of diagnostic VHH-Fc antibodies in Nicotiana benthamiana leaves with their stable expression in Arabidopsis thaliana seeds and Pichia pastoris. To this end, VHH-Fc antibodies targeting green fluorescent protein or the A. thaliana seed storage proteins (albumin and globulin) were produced in the three platforms. Differences were mainly observed in the accumulation levels and glycosylation patterns. Interestingly, although in plants oligomannosidic N-glycans were expected for KDEL-tagged VHH-Fcs, several VHH-Fcs with an intact KDEL-tag carried complex-type N-glycans, suggesting a dysfunctional retention in the endoplasmic reticulum. All VHH-Fcs were equally functional across expression platforms and several outperformed their corresponding VHH in terms of sensitivity in ELISA.
Crack Toughness Behaviour of Multiwalled Carbon Nanotube (MWNT)/Polycarbonate Nanocomposites

The morphology and fracture behaviour of polycarbonate (PC)/multiwalled carbon nanotube(MWNT) composites have been studied by AFM and post-yield fracture mechanics. The essential work of fracture (EWF) method has been used to distinguish between two terms representing the resistance to crack initiation and crack propagation. A maximum in the non-essential work of fracture was observed at 2 wt. -% MWNT, demonstrating enhanced resistance to crack propagation compared to pure PC. At 4 wt. -% MWNT, a tough-to-brittle transition has been observed. The time-resolved in-situ strain field analysis revealed that the onset of crack initiation was shifted to a shorter time for nanocomposites with 4 wt. -% MWNT compared to that with 2 wt. -%, and thus explained the existence of a tough-to-brittle transition in these nanocomposites.
Direction finding in random inhomogeneous media in the presence of multiplicative noise

The performances of high resolution array processing methods are known to degrade in random inhomogeneous media. Such a degradation is caused by random amplitude and phase variations of source wavefronts. In this letter, the popular covariance matching approach to direction finding in the presence of multiplicative noise is extended to the multiple source case. Using a few unrestrictive physics-based assumptions on the environment, we derive a generic multiplicative noise data model. Based on this model, new direction finding techniques are proposed.
Stem Cell Antigen-1 in Skeletal Muscle Function

Stem cell antigen-1 (Sca-1) is a member of the Ly-6 multigene family encoding highly homologous, glycosyl-phosphatidylinositol-anchored membrane proteins. Sca-1 is expressed on muscle-derived stem cells and myogenic precursors recruited to sites of muscle injury. We previously reported that inhibition of Sca-1 expression stimulated myoblast proliferation in vitro and regulated the tempo of muscle repair in vivo. Despite its function in myoblast expansion during muscle repair, a role for Sca-1 in normal, post-natal muscle has not been thoroughly investigated. We systematically compared Sca-1-/- (KO) and Sca-1+/+ (WT) mice and hindlimb muscles to elucidate the tissue, contractile, and functional effects of Sca-1 in young and aging animals. Comparison of muscle volume, fibrosis, myofiber cross-sectional area, and Pax7+ myoblast number showed little differences between ages or genotypes. Exercise protocols, however, demonstrated decreased stamina in KO versus WT mice, with young KO mice achieving results similar to aging WT animals. In addition, KO mice did not improve with practice, while WT animals demonstrated conditioning over time. Surprisingly, myomechanical analysis of isolated muscles showed that KO young muscle generated more force and experienced less fatigue. However, KO muscle also demonstrated incomplete relaxation with fatigue. These findings suggest that Sca-1 is necessary for muscle conditioning with exercise, and that deficient conditioning in Sca-1 KO animals becomes more pronounced with age.
Hand X-ray in pediatric endocrinology: Skeletal age assessment and beyond

Skeletal age assessment (SAA) is a clinical procedure which is used in determining the SA of children and adolescents. Bone development is influenced by a number of factors, including nutrition, hormonal secretions, and genetics. There are several factors to be borne in mind when using methods of assessing skeletal maturity. These include: Variability among methods, degree of variability in the estimation of skeletal maturation, sources of low accuracy, and dispersion of the values of skeletal maturation. Currently, the main clinical methods for SAA are the Greulich and Pyle (GP) and Tanner and Whitehouse (TW) methods. The GP method has the advantage of being quick and easy to use. A well-trained radiologist takes few minutes to determine the bone age (BA) from a single hand radiograph. The method of TW, however, seems to be more reliable than the GP method. In recent years, the increasing speed in computer sciences and reduction of their cost has given the opportunity to create and use computerized BA estimation system. Despite the fact that the number of automated systems for BAA have increased, most are still within the experimental phase. The use of automated BA determination system, cleared for clinical use in Europe (BoneXpert), has been validated for various ethnicities and children with endocrine disorders. Ultrasound imaging has some limitations that include operator dependence, lower intra-rater and inter-rater reliability of assessment and difficulties with standardization of documentation and imaging transfer. Magnetic resonance imaging (MRI) is noninvasive alternative tool for SA assessment in children. However, few studies have been reported on this topic, and further research is needed to evaluate the reliability and validity of MRI BAAs. In conclusion, at present radiographic methods for the assessment of BA remain the gold standards. Whatever method one adopts, it is essential to minimize the causes of imprecision by taking care to consider the quality of the X-ray. Moreover, it is imperative to assume a correct hand positioning because poor positioning can change the appearance of some bones. It is also preferable to employ scoring methods to these techniques and percentiles rather than BA in years and months. In addition, the possible differences in maturation among different population should be kept in mind.
Conductive Hearing Loss Disrupts Synaptic and Spike Adaptation in Developing Auditory Cortex

Although sensorineural hearing loss (SNHL) is known to compromise central auditory structure and function, the impact of milder forms of hearing loss on cellular neurophysiology remains mostly undefined. We induced conductive hearing loss (CHL) in developing gerbils, reared the animals for 8–13 d, and subsequently assessed the temporal features of auditory cortex layer 2/3 pyramidal neurons in a thalamocortical brain slice preparation with whole-cell recordings. Repetitive stimulation of the ventral medial geniculate nucleus (MGv) evoked robust short-term depression of the postsynaptic potentials in control neurons, and this depression increased monotonically at higher stimulation frequencies. In contrast, CHL neurons displayed a faster rate of synaptic depression and a smaller asymptotic amplitude. Moreover, the latency of MGv evoked potentials was consistently longer in CHL neurons for all stimulus rates. A separate assessment of spike frequency adaptation in response to trains of injected current pulses revealed that CHL neurons displayed less adaptation compared with controls, although there was an increase in temporal jitter. For each of these properties, nearly identical findings were observed for SNHL neurons. Together, these data show that CHL significantly alters the temporal properties of auditory cortex synapses and spikes, and this may contribute to processing deficits that attend mild to moderate hearing loss.