Miracle-dz/UniFAR-FTUs huggingface dataset:
Stoichiometry of Envelope Glycoprotein Trimers in the Entry of Human Immunodeficiency Virus Type 1

ABSTRACT The human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins (Envs) function as a trimer, mediating virus entry by promoting the fusion of the viral and target cell membranes. HIV-1 Env trimers induce membrane fusion through a pH-independent pathway driven by the interaction between an Env trimer and its cellular receptors, CD4 and CCR5/CXCR4. We studied viruses with mixed heterotrimers of wild-type and dominant-negative Envs to determine the number (T) of Env trimers required for HIV-1 entry. To our surprise, we found that a single Env trimer is capable of supporting HIV-1 entry; i.e., T = 1. A similar approach was applied to investigate the entry stoichiometry of envelope glycoproteins from amphotropic murine leukemia virus (A-MLV), avian sarcoma/leukosis virus type A (ASLV-A), and influenza A virus. When pseudotyped on HIV-1 virions, the A-MLV and ASLV-A Envs also exhibit a T = 1 entry stoichiometry. In contrast, eight to nine influenza A virus hemagglutinin trimers function cooperatively to achieve membrane fusion and virus entry, using a pH-dependent pathway. The different entry requirements for cooperativity among Env trimers for retroviruses and influenza A virus may influence viral strategies for replication and evasion of the immune system.
Architecture for automation system development based on IEC 61499 standard

This paper introduces an idea of a validatable architecture for software intensive industrial automation systems. The validation means will be provided through the formal modeling of automation systems, including both modeling of uncontrolled behavior of the equipment and modeling of the control system. This will be achieved through the facilitated reuse and integration of basic models to the models of complex systems. The validation will be empowered by advanced formal verification techniques combined with more usual testing by simulation. The discussed architecture bases on the latest developments in automation such as IEC 61499 standard, on the latest trends in model-based software engineering, e.g. UML, and on modular modeling concepts of condition/event systems.
Autism, language delay and mental retardation in a patient with 7q11 duplication

Chromosomal rearrangements are found in a subset of patients with autism. Duplications involving loci associated with behavioural disturbances constitute an especially good candidate mechanism. The Williams–Beuren critical region (WBCR), located at 7q11.23, is commonly deleted in Williams–Beuren microdeletion syndrome (WBS). However, only four patients with a duplication of the WBCR have been reported to date. Here, 206 patients with autism spectrum disorders were screened for the WBCR duplication by quantitative microsatellite analysis and multiple ligation-dependent probe amplification. One male patient with a de novo interstitial duplication of the entire WBCR of paternal origin was identified. The patient had autistic disorder, severe language delay and mental retardation, with mild dysmorphism. The present report concerns the first patient with autistic disorder and a WBCR duplication. This observation indicates that the 7q11.23 duplication could be involved in complex clinical phenotypes, ranging from developmental or language delay to mental retardation and autism.
Structural Organization and Regulation of the Small Proline-rich Family of Cornified Envelope Precursors Suggest a Role in Adaptive Barrier Function*

The protective barrier provided by stratified squamous epithelia relies on the cornified cell envelope (CE), a structure synthesized at late stages of keratinocyte differentiation. It is composed of structural proteins, including involucrin, loricrin, and the small proline-rich (SPRR) proteins, all encoded by genes localized at human chromosome 1q21. The genetic characterization of the SPRR locus reveals that the various members of this multigene family can be classified into two distinct groups with separate evolutionary histories. Whereas group 1 genes have diverged in protein structure and are composed of three different classes (SPRR1 (2×), SPRR3, and SPRR4), an active process of gene conversion has counteracted diversification of the protein sequences of group 2 genes (SPRR2 class, seven genes). Contrasting with this homogenization process, all individual members of the SPRR gene family show specific in vivo and in vitro expression patterns and react selectively to UV irradiation. Apparently, creation of regulatory rather than structural diversity has been the driving force behind the evolution of the SPRR gene family. Differential regulation of highly homologous genes underlines the importance of SPRR protein dosage in providing optimal barrier function to different epithelia, while allowing adaptation to diverse external insults.
An Increased Number of Follicles Containing Activated CD69+ Helper T Cells and Proliferating CD71+ B Cells Are Found in H. pylori-Infected Gastric Mucosa

Objective:An immune response occurring in Helicobacter pylori-infected gastric mucosa could have a direct implication for associated pathologies. In the present study we analyzed the expression of the immune activation, proliferation, and phenotype markers by immune cell subpopulations in H. pylori-infected and uninfected gastric samples.Methods:Antral gastric biopsies from both H. pylori-positive and -negative patients were processed by immunohistochemistry; gastric epithelial cells were isolated from biopsy tissue and analyzed by flow cytometry.Results:Ten of the 13 biopsies that contained follicles were H. pylori positive. Follicular CD69 was expressed mainly by CD4+ T cells and the central core of follicles showed double immunopositivity for the B-cell marker CD19 and transferrin receptor. Also detected was an increase in the percentage of epithelial cells from H. pylori-positive samples expressing HLA-DR and β2 microglobulin, compared to negative samples (61 ± 15%vs 9 ± 9%, p= 0.003 and 93 ± 7%vs 52 ± 18%, p= 0.002, respectively), whereas no variation on class I HLA was detected. Conclusions: These results suggest that chronic H. pylori infection could facilitate the persistance of follicles on which continuous follicular helper T-cell activation could lead to uncontrolled follicular B-cell proliferation. Furthermore, β2 microglobulin expression by epithelial cells in a nonparallel way to class I HLA may indicate the possibility of nonclassical class I MHC expression on the basal surface of the epithelium.
Transcription factor JunD, deprived of menin, switches from growth suppressor to growth promoter

Different components of the AP1 transcription factor complex appear to have distinct effects on cell proliferation and transformation. In contrast to other AP1 components, JunD has been shown to inhibit cell proliferation. Also, in prior studies, JunD alone bound menin, product of the MEN1 tumor suppressor gene, and JunD's transcriptional activity was inhibited by menin, suggesting that JunD might achieve all or most of its unique properties through binding to menin. Analyses of JunD and menin effects on proliferation, morphology, and cyclin D1 in stable cell lines unmasked an unexpected growth promoting activity of JunD. Whereas stable overexpression of wild-type (wt) mouse JunD in JunD–/– immortalized fibroblasts inhibited their proliferation and reverted their transformed-like phenotype, overexpression of a missense mouse JunD mutant (mJunDG42E) with disabled binding to menin showed opposite or growth promoting effects. Similarly, stable overexpression of wt mouse JunD in wt immortalized fibroblasts inhibited growth. In contrast, its overexpression in Men1–/– immortalized fibroblasts enhanced their already transformed-like characteristics. To conclude, JunD changed from growth suppressor to growth promoter when its binding to menin was prevented by a JunD mutant unable to bind menin or by Men1-null genetic background.
Scattering Properties of Carbon Nanotube Arrays

Interaction of carbon nanotubes (CNTs) with electromagnetic waves has not been extensively investigated, nor is well understood. In this paper, we examine the scattering behavior of finite CNTs arrays at terahertz frequencies. To this end, we employ a method of moment (MoM) analysis in conjunction with the thin wire approximation capable of analyzing complex geometries in a few minutes on a standard portable PC. MoM analysis and relevant numerical code is evaluated against published results and excellent agreement is observed. To fully understand scattering properties of CNT arrays, we keep the structures simple, yet valuable results are extracted. Arrays comprise parallel elements and are illuminated by a plane wave. Apart from scattering properties and patterns, current profiles are also quantified and plotted. This analysis and the results extracted are expected to prove useful in the future as a reference for electromagnetic shielding applications.
Nerve biopsy findings in different patterns of proximal diabetic neuropathy

Besides distal symmetrical sensory polyneuropathy (DSSP), middle‐aged diabetic patients may present with focal or multifocal neuropathies, including proximal neuropathy of the lower limbs, the pathophysiological features of which are uncertain. We studied 10 non–insulin‐dependent diabetic patients, 45 to 72 years of age, who developed a painful proximal neuropathy of the lower limbs for which other causes of neuropathy were carefully excluded. The proximal neuropathy was asymmetrical in all patients, sensory in 4, motor and sensory in the others. Signs of DSSP were present in all. A sample of the intermediate cutaneous nerve of the thigh, a sensory branch of the femoral nerve, was taken by biopsy and examined by light and electron microscopy. Examination of the nerve specimens revealed ischemic nerve lesions in 3 patients. Nerve ischemia was associated with vasculitis and inflammatory infiltration in 2 of them. In the other patients the lesions of the cutaneous nerve of the thigh included a varying incidence of axonal and demyelinative lesions similar to those observed in DSSP, with mild inflammatory infiltration in 4 of them. The density of myelinated and of unmyelinated was variably decreased. This study shows that axonal and demyelinative lesions similar to those found in diabetic DSSP are present in proximal nerves in mild forms of proximal diabetic neuropathy; while nerve ischemia, inflammatory infiltration, and vasculitis are encountered in the most severe forms of proximal diabetic neuropathy.
A Digital Pulse Library for the Optimization of Signal Processing in PET

In this work, we developed a comprehensive digital pulse library as a reference data set, against which the performance of pulse processing algorithms can be evaluated. The pulses are directly recorded from real measurements with scintillation detectors multiplexed by a resistor divider network. This way, the pulses better represent systematic variations of detection sensitivity for detector panels due to differences in light sharing, light collection and crystal scatter among other effects. The pulse shapes exactly represent the signals to be processed in the data acquisition and signal processing unit, but for which the ground truth regarding energy, position and timing can be known. A conventional pulse pileup rejection method called leading edge rejection (LER) was evaluated with the help of the pulse library. The simulated pulse library based results show that the LER method can effectively suppress most of the pileup caused mispositioned events, while it also trades off against sensitivity loss. Physical measurements agree with the pulse library simulation results. In conclusion, the proposed evaluation method based on digital pulse library can significantly reduce the time and effort invested in the development and optimization of various signal processing algorithms.
Homeostasis of memory T cells

Summary: The pool of memory T cells is regulated by homeostatic mechanisms to persist for prolonged periods at a relatively steady overall size. Recent work has shown that two members of the common γ chain (γc) family of cytokines, interleukin‐7 (IL‐7) and IL‐15, govern homeostasis of memory T cells. These two cytokines work in conjunction to support memory T‐cell survival and intermittent background proliferation. Normal animals contain significant numbers of spontaneously arising memory‐phenotype (MP) cells, though whether these cells are representative of true antigen‐specific memory T cells is unclear. Nevertheless, it appears that the two types of memory cells do not display identical homeostatic requirements. For antigen‐specific memory CD8+ T cells, IL‐7 is primarily important for survival while IL‐15 is crucial for their background proliferation. For memory CD4+ T cells, IL‐7 has an important role, whereas the influence of IL‐15 is still unclear.
A 1.8-V 6.9-mW 120-fps 50-Channel Capacitive Touch Readout With Current Conveyor AFE and Current-Driven $\Delta \Sigma $ ADC

This paper presents an area- and energy-efficient readout for capacitive touch sensors. An analog front end (AFE) with current conveyor mitigates the requirements of front-end opamp and provides a differential current from adjacent channels, removing sensor’s baseline and interferences. The sensing current from the AFE is directly digitized by a current-driven 2nd-order <inline-formula> <tex-math notation="LaTeX">$\Delta \Sigma $ </tex-math></inline-formula> analog-to-digital converter and its direct interfacing with the current signal achieves high signal-to-noise ratio (SNR) without suffering voltage saturation in the AFE, and provides reconfigurable SNRs and frame rates with respect to oversampling ratio. An area-efficient sinc<sup>2</sup> filter, whose filter coefficients are commonly provided, enables full parallel implementation of <inline-formula> <tex-math notation="LaTeX">$\Delta \Sigma $ </tex-math></inline-formula> ADCs. A 50-channel prototype IC is fabricated in a 0.18-<inline-formula> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> CMOS process, occupying only 1.96 mm<sup>2</sup>. Using a 10.1-in <inline-formula> <tex-math notation="LaTeX">$28 \times 50$ </tex-math></inline-formula> touch screen panel and a 3.3-V transmitter, this work achieves SNRs of 53.3 and 41.7 dB with finger and 1-mm-<inline-formula> <tex-math notation="LaTeX">$\phi $ </tex-math></inline-formula> stylus, respectively, while drawing only 6.9 mW from 1.8-V supply at 120 fps. This results in the state-of-the-art figure-of-merit of 0.11 and 0.41 nJ/step for finger and 1-mm-<inline-formula> <tex-math notation="LaTeX">$\phi $ </tex-math></inline-formula> stylus, respectively. Moreover, 500-dpi on-glass fingerprint sensor is verified with the same prototype IC and 15-V transmitter, and <inline-formula> <tex-math notation="LaTeX">$70 \times 50$ </tex-math></inline-formula> fingerprint image is successfully captured with 150-<inline-formula> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> cover glass.
Health Effects of Probiotics on the Skin

Skin is the largest organ of the body and is constantly exposed to physical, chemical, bacterial, and fungal challenges. It is well known that probiotics are helpful for specific disorders and different clinical studies have indicated that probiotics have special effects in cutaneous apparatus directly or indirectly that can be considerable from versatile aspects. Probiotic bacteriotherapy can have great potential in preventing and treating the skin diseases including eczema, atopic dermatitis, acne, and allergic inflammation or in skin hypersensitivity, UV-induced skin damage, wound protection, and as a cosmetic product. The current paper comprehensively reviews the different health effects of probiotics on the skin.
Vertical transmission of tissue microbiota in Caenorhabditis elegans

The past forty-five years has witnessed Caenorhabditis elegans as the most significant model animal in life science since its discovery seventy years ago1,2, as it introduced principles of gene regulated organ development, and RNA interference into biology3-5. Meanwhile, it has become one of the lab animals in gut microbiota studies as these symbionts contribute significantly to many aspects in host biology6,7. Meanwhile, the origin of gut microbiota remains debatable in human8- 11, and has not been investigated in other model animals. Here we show that the symbiont bacteria in C. elegans not only vertically transmit from the parent generation to the next, but also distributes in the worm tissues parallel with its development. We found that bacteria can enter into the embryos of C. elegans, a step associated with vitellogenin, and passed to the next generation. These vertically transmitted bacteria share global similarity, and bacterial distribution in worm tissues changes as they grow at different life stages. Antibiotic treatment of worms increased their vulnerability against pathogenic bacteria, and replenishment of tissue microbiota restored their immunity. These results not only offered a molecular basis of vertical transmission of bacteria in C. elegans, but also signal a new era for the mixed tissue cell-bacteria multi-species organism study.
Converting Education into Income and Occupational Status

This article extends an earlier investigation of differences among European immigrant groups in the United States in the extent to which they convert educational attainment into income. The size of the sample has been significantly enlarged, making it possible to include more ethnic groups and to increase the number of factors taken into account. The present analysis examines the conversion of educational achievement into income and into occupational status. Special attention is focused on the earlier finding that, among second-generation immigrants, those with only the father foreign born are most effective in converting education into earnings.
High-Throughput Confocal Imaging of Intact Live Tissue Enables Quantification of Membrane Trafficking in Arabidopsis1[W]

Membrane compartmentalization and trafficking within and between cells is considered an essential cellular property of higher eukaryotes. We established a high-throughput imaging method suitable for the quantitative detection of membrane compartments at subcellular resolution in intact epidermal tissue. Whole Arabidopsis (Arabidopsis thaliana) cotyledon leaves were subjected to quantitative confocal laser microscopy using automated image acquisition, computational pattern recognition, and quantification of membrane compartments. This revealed that our method is sensitive and reliable to detect distinct endomembrane compartments. We applied quantitative confocal laser microscopy to a transgenic line expressing GFP-2xFYVE as a marker for endosomal compartments during biotic or abiotic stresses, and detected markedly quantitative adaptations in response to changing environments. Using a transgenic line expressing the plasma membrane-resident syntaxin GFP-PEN1, we quantified the pathogen-inducible extracellular accumulation of this fusion protein at fungal entry sites. Our protocol provides a platform to study the quantitative and dynamic changes of endomembrane trafficking, and potential adaptations of this machinery to physiological stress.
Inhibition of Recombinant Human T-type Calcium Channels by Δ9-Tetrahydrocannabinol and Cannabidiol*

Δ9-Tetrahydrocannabinol (THC) and cannabidiol (CBD) are the most prevalent biologically active constituents of Cannabis sativa. THC is the prototypic cannabinoid CB1 receptor agonist and is psychoactive and analgesic. CBD is also analgesic, but it is not a CB1 receptor agonist. Low voltage-activated T-type calcium channels, encoded by the CaV3 gene family, regulate the excitability of many cells, including neurons involved in nociceptive processing. We examined the effects of THC and CBD on human CaV3 channels stably expressed in human embryonic kidney 293 cells and T-type channels in mouse sensory neurons using whole-cell, patch clamp recordings. At moderately hyperpolarized potentials, THC and CBD inhibited peak CaV3.1 and CaV3.2 currents with IC50 values of ∼1 μm but were less potent on CaV3.3 channels. THC and CBD inhibited sensory neuron T-type channels by about 45% at 1 μm. However, in recordings made from a holding potential of -70 mV, 100 nm THC or CBD inhibited more than 50% of the peak CaV3.1 current. THC and CBD produced a significant hyperpolarizing shift in the steady state inactivation potentials for each of the CaV3 channels, which accounts for inhibition of channel currents. Additionally, THC caused a modest hyperpolarizing shift in the activation of CaV3.1 and CaV3.2. THC but not CBD slowed CaV3.1 and CaV3.2 deactivation and inactivation kinetics. Thus, THC and CBD inhibit CaV3 channels at pharmacologically relevant concentrations. However, THC, but not CBD, may also increase the amount of calcium entry following T-type channel activation by stabilizing open states of the channel.
Influence of Maternal Xylitol Consumption on Acquisition of Mutans Streptococci by Infants

Xylitol is effective as a non-cariogenic sugar substitute. Habitual xylitol consumption appears to select for mutans streptococci (MS) with impaired adhesion properties, i.e., they shed easily to saliva from plaque. One hundred sixty-nine mother-child pairs participated in a two-year study exploring whether the mothers' xylitol consumption could be used to prevent mother-child transmission of mutans streptococci. All mothers showed high salivary levels of mutans streptococci during pregnancy. The mothers in the xylitol group (n = 106) were requested to chew xylitol-sweetened gum (65% w/w) at least 2 or 3 times a day, starting three months after delivery. In the two control groups, the mothers received either chlorhexidine (n = 30) or fluoride (n = 33) varnish treatments at 6, 12, and 18 months after delivery. The children did not chew gum or receive varnish treatments. MS were assessed from the mothers' saliva at half-year intervals and from the children's plaque at the one- and two-year examinations. The MS were cultured on Mitis salivarius agars containing bacitracin. The salivary MS levels of the mothers remained high and not significantly different among the three study groups throughout the study. At two years of age, 9.7% of the children in the xylitol, 28.6% in the chlorhexidine, and 48.5% in the fluoride varnish group showed a detectable level of MS. In conclusion, therefore, habitual xylitol consumption by mothers was associated with a statistically significant reduction of the probability of mother-child transmission of MS assessed at two years of age. The effect was superior to that obtained with either chlorhexidine or fluoride varnish treatments performed as single applications at six-month intervals.
Self management of a mobile thin client service

Mobile thin client computing is an enabler for the execution of demanding applications from mobile handhelds. In thin client computing, the application is executed on remote servers and the mobile handheld only has to display the graphical updates and send input from the user to the remote execution environment. To guarantee a high user experience in a mobile environment, a Service Management Framework is required to prevent users observing lower Quality of Experience due to changes in the available network, server and client resources. Therefore, the Service Management Framework monitors the environment and the Self Management component intervenes when necessary, e.g. by adapting the thin client protocol settings or moving a user session from one server to another. The design of the Self Management component is presented and the performance is evaluated.