Miracle-dz/UniFAR-FTUs huggingface dataset:
Significantly Longer Envelope V2 Loops Are Characteristic of Heterosexually Transmitted Subtype B HIV-1 in Trinidad

Background In Trinidad and the wider Caribbean, subtype B Human Immunodeficiency Virus-type 1 (HIV-1B) overwhelmingly accounts for HIV infection among heterosexuals; this contrasts with the association of HIV-1B with homosexual transmission and injecting drug use globally. The HIV envelope contains genetic determinants of cell tropism and evasion from immune attack. In this study we investigate the genetic properties of the env V1-C4 of HIV-1B soon after transmission to Trinidadian heterosexuals. This will reveal distinctive genetic features of the strains that cause the HIV-1B epidemic in Trinidad and generate insights to better understand their properties. Methodology/Principal Findings Quasispecies sampling was performed on the env V1-C4 of HIV-1B strains soon after transmission to heterosexual Trinidadians in a cohort of seroconverters. Phylogenetic relationships were determined for these quasispecies and the length and number of asparagine (N) linked glycosylation sites (NLGS) in their variable loops compared to that for HIV-1B globally. Signature amino acids within the constant domains of the env V1-C4 were identified for heterosexually transmitted HIV-1B from Trinidad relative to HIV-1B globally. HIV-1B obtained from Trinidadian heterosexuals soon after seroconversion had significantly longer V2 loops with one more glycosylation site, shorter V3 loops and no significant difference in V1 or V4 when compared to HIV-1B obtained soon after seroconversion from infected individuals in the rest of the world. HIV-1B soon after seroconversion and during chronic infection of Trinidadians was not significantly different, suggesting that distinctly long V2 loops are characteristic of HIV-1B in Trinidad. A threonine deletion at position 319 (T319-) along with the substitutions R315K and S440R were found to be distinctly associated with HIV-1B from Trinidad compared to HIV-1B globally. Conclusions This finding of distinctive genetic features that are characteristic of HIV-1B strains from Trinidad is consistent with the Trinidad epidemic being established by a founder strain or closely related founder strains of HIV-1B.
CaMKIIdelta subtypes: localization and function

In this review we discuss the localization and function of the known subtypes of calcium/calmodulin dependent protein kinase IIδ (CaMKIIδ) and their role in cardiac physiology and pathophysiology. The CaMKII holoenzyme is comprised of multiple subunits that are encoded by four different genes called CaMKIIα, β, γ, and δ. While these four genes have a high degree of sequence homology, they are expressed in different tissues. CaMKIIα and β are expressed in neuronal tissue while γ and δ are present throughout the body, including in the heart. Both CaMKIIγ and δ are alternatively spliced in the heart to generate multiple subtypes. CaMKIIδ is the predominant cardiac isoform and is alternatively spliced in the heart to generate the CaMKIIδB subtype or the slightly less abundant δC subtype. The CaMKIIδB mRNA sequence contains a 33bp insert not present in δC that codes for an 11-amino acid nuclear localization sequence. This review focuses on the localization and function of the CaMKIIδ subtypes δB and δC and the role of these subtypes in arrhythmias, contractile dysfunction, gene transcription, and the regulation of Ca2+ handling.
Efficient Spurious Rejection and Null Steering Using Slot Antennas

Reconfigurable antennas are susceptible to spurious signal reception through feed lines, interconnects and connector transitions. In this letter, a two-slot antenna backed by a metal box is demonstrated, where such spurious signals are not picked up and, consequently, spurious rejection is very high. It is shown that the direction from which signals are strongly rejected is also switchable. Finally, a four-slot array for rejecting spurious signals over some angular range, rather than at a specific angle, is presented .
Central Corneal Thickness Measurements with Optical Coherence Tomography and Ultrasound Pachymetry in Healthy Subjects and in Patients after Photorefractive Keratectomy

Purpose To compare central corneal thickness measurements made using two different methods, optical coherence tomography (OCT) and ultrasound pachymetry, applied both in normal eyes and in eyes on which photorefractive keratectomy (PRK) had been performed. A second objective was to assess the intrasession variability of OCT measurements. Methods In this prospective study, central corneal thickness was measured in 20 normal subjects (normal group) and in 20 PRK patients using the StratusOCT instrument model 3000 (Carl Zeiss Meditec), and also with an ultrasound pachymeter. Five OCT measurements were performed using the Fast Macular Thickness protocol. Corneal thickness data were obtained with the Scan Profile analysis protocol. The OCT measurement results were compared with the mean value of three ultrasound pachymetry measurements for the same eye. Results The pachymetry–OCT correlation coefficients were 0.96 and 0.97 in the normal and PRK groups, respectively (p=0.14). Neither linear regression nor Bland-Altmann analysis revealed any significant systematic measurement error. Intrasession standard deviations in the normal and PRK groups were 4.9 μm and 3.8 μm, respectively. Conclusions Noncontact central corneal thickness measurements made using the StratusOCT instrument are accurate and reproducible, both in normal subjects and in post-PRK patients. The instrument system does not need any modifications to correctly detect and measure the center of the cornea.
Divergent transcriptional responses to low temperature among populations of alpine and lowland species of New Zealand stick insects (Micrarchus)

In widespread and genetically structured populations, temperature variation may lead to among‐population differentiation of thermal biology. The New Zealand stick insect genus Micrarchus contains four species that inhabit different thermal environments, two of which are geographically widespread. RNA‐Seq and quantitative PCR were used to investigate the transcriptional responses to cold shock among lowland and alpine species to identify cold‐responsive transcripts that differ between the species and to determine whether there is intraspecific geographical variation in gene expression. We also used mitochondrial DNA, nuclear 28S ribosomal DNA and transcriptome‐wide SNPs to determine phylogeographic structure and the potential for differences in genetic backgrounds to contribute to variation in gene expression. RNA‐Seq identified 2160 unigenes that were differentially expressed as a result of low‐temperature exposure across three populations from two species (M. hystriculeus and M. nov. sp. 2), with a majority (68% ± 20%) being population specific. This extensive geographical variation is consistent across years and is likely a result of background genetic differences among populations caused by genetic drift and possibly local adaptation. Responses to cold shock shared among alpine M. nov. sp. 2 populations included the enrichment of cuticular structure‐associated transcripts, suggesting that cuticle modification may have accompanied colonization of low‐temperature alpine environments and the development of a more cold‐hardy phenotype.
NEW MOLECULAR DATA ON MAMMALIAN HEPATOZOON SPECIES (APICOMPLEXA: ADELEORINA) FROM BRAZIL AND SPAIN

Molecular techniques were used to examine the phylogenetic relationships among Hepatozoon species isolated from 13 foxes and 15 opossums from Brazil, and from 15 dogs, 20 foxes, 45 rodents, and 330 domestic cats from Spain. Hemogregarine infection was confirmed by amplification of the 18S rRNA gene and later sequencing. No hemogregarine infections were found in opossums. The prevalence of Hepatozoon in canids ranged from 26.6% (symptomatic domestic dogs) to 90% (Spanish foxes). Four different H. canis genotypes were detected, as well as an H. americanum-related protozoan (97% identical to the USA strain). Two Spanish cats were parasitized by a Hepatozoon species (0.6% prevalence) that showed 96% sequence identity to H. canis. DNA amplification assays performed on Spanish rodents showed 2 bank voles (Clethrionomys glareolus) to be infected by a Hepatozoon species (4.44% prevalence) with 95% sequence identity to Hepatozoon sp. from cats. Phylogenetic analysis showed Hepatozoon to be a monophyletic genus, in which species from carnivorous mammals (Hepatozoon sp. from cats, H. americanum and H. canis) appear as a sister lineage of that of lower vertebrates and rodents. This association suggests that H. americanum evolved in ticks and carnivores (either canids, or felids, or both) rather than in other ectoparasites and other types of mammal.
Informal Concepts in Machines

This paper constructively proves the existence of an effective procedure generating a computable (total) function that is not contained in any given effectively enumerable set of such functions. The proof implies the existence of machines that process informal concepts such as computable (total) functions beyond the limits of any given Turing machine or formal system, that is, these machines can, in a certain sense, "compute" function values beyond these limits. We call these machines creative. We argue that any "intelligent" machine should be capable of processing informal concepts such as computable (total) functions, that is, it should be creative. Finally, we introduce hypotheses on creative machines which were developed on the basis of theoretical investigations and experiments with computer programs. The hypotheses say that machine intelligence is the execution of a self-developing procedure starting from any universal programming language and any input.
Construct robust rule sets for classification

We study the problem of computing classification rule sets from relational databases so that accurate predictions can be made on test data with missing attribute values. Traditional classifiers perform badly when test data are not as complete as the training data because they tailor a training database too much. We introduce the concept of one rule set being more robust than another, that is, able to make more accurate predictions on test data with missing attribute values. We show that the optimal class association rule set is as robust as the complete class association rule set. We then introduce the k-optimal rule set, which provides predictions exactly the same as the optimal class association rule set on test data with up to k missing attribute values. This leads to a hierarchy of k-optimal rule sets in which decreasing size corresponds to decreasing robustness, and they all more robust than a traditional classification rule set. We introduce two methods to find k-optimal rule sets, i.e. an optimal association rule mining approach and a heuristic approximate approach. We show experimentally that a k-optimal rule set generated by the optimal association rule mining approach performs better than that by the heuristic approximate approach and both rule sets perform significantly better than a typical classification rule set (C4.5Rules) on incomplete test data.
Who Decides? The Connecting Thread of Euthanasia, Eugenics, and Doctor-Assisted Suicide

Throughout recorded history, a series of seemingly unrelated ideas have been consistently intertwined: suicide, euthanasia, infanticide, eugenics, genocide and, most recently, the practice termed physician-assisted suicide. From Plato and Hippocrates to a pair of twentieth-century American physicians named Haiselden and Kevorkian, an examination of history shows these disparate notions always involve two troublesome questions: Which lives are not worth living? And who will decide? The same examination of history teaches that separating the worthy from the not worthy is a very dangerous proposition, especially for those whose lives are deemed marginal.
Association of Hepatitis C Virus With Insulin Resistance: Evidences From Animal Studies and Clinical Studies

Context HCV infection is strongly associated with development of insulin resistance and type-2 diabetes, however molecular mechanism of these associations is not known. The aim of this review was to conduct a comprehensive literature search to understand the nature of the association between hepatitis C virus (HCV) infection and insulin resistance (IR). We also explored the role of HCV core protein and NS5a in modulating the course of the insulin-signaling pathway. Evidence Acquisitions We searched Directory of Open Access Journals (DOAJ) Google Scholar, Pubmed (NLM), LISTA (EBSCO), Web of Science (TS and PakMediNet). Results Emerging evidence suggests an association between HCV infection and carotid/coronary vascular disease. IR appears to be a dominant underlying cause of accelerated atherosclerosis in patients with chronic hepatitis C (CHC). HCV can induce IR directly through the stimulation of SOCS3 and PPA2, and both of these molecules have been shown to inhibit interferon-α signaling. Improvement of insulin sensitivity may increase the response rate to antiviral treatment and prevent IR complications, including vascular diseases. The results of several clinical trials that have used insulin sensitizers (metformin and PPAR-γ agonists) have been inconclusive. Conclusions Beside the association between HCV and IR, the published data also have showed the possible association of HCV core and NS5A protein with IR.
Altered MicroRNA Expression Profile in Exosomes during Osteogenic Differentiation of Human Bone Marrow-Derived Mesenchymal Stem Cells

The physiological role of microRNAs (miRNAs) in osteoblast differentiation remains elusive. Exosomal miRNAs isolated from human bone marrow-derived mesenchymal stem cells (BMSCs) culture were profiled using miRNA arrays containing probes for 894 human matured miRNAs. Seventy-nine miRNAs (∼8.84%) could be detected in exosomes isolated from BMSC culture supernatants when normalized to endogenous control genes RNU44. Among them, nine exosomal miRNAs were up regulated and 4 miRNAs were under regulated significantly (Relative fold>2, p<0.05) when compared with the values at 0 day with maximum changes at 1 to 7 days. Five miRNAs (miR-199b, miR-218, miR-148a, miR-135b, and miR-221) were further validated and differentially expressed in the individual exosomal samples from hBMSCs cultured at different time points. Bioinformatic analysis by DIANA-mirPath demonstrated that RNA degradation, mRNA surveillance pathway, Wnt signaling pathway, RNA transport were the most prominent pathways enriched in quantiles with differential exosomal miRNA patterns related to osteogenic differentiation. These data demonstrated exosomal miRNA is a regulator of osteoblast differentiation.
Towards Optimized Probe Scheduling for Active Measurement Studies

—Internet measurement studies often require prolonged probing of remote targets to collect information, yet almost all such studies of which we are aware were undertaken without considering the polluting effects of their unconstrained probing behavior. To help researchers conduct experiments in a more responsible fashion, we present a framework and technique that enables efﬁcient execution of large-scale periodic probing without exceeding pre-set limits on probing rates. Our technique employs a novel scheduling algorithm and leverages knowledge of diurnal trafﬁc patterns to make data collection more efﬁcient (e.g., by probing servers only during periods in which probe results will be most useful). We evaluate our technique in the context of a real-world study and show that it substantially outperforms na¨ıve probing strategies for accomplishing the same goal, sending more probes during useful periods, fewer probes overall, and probing at more precise intervals as required by our measurement applications.
Obstacles in object-oriented software development

Recently, a considerable number of object-oriented software development methods have been introduced to produce extensible, reusable, and robust software. We have been involved in the development of a large number of pilot applications to form our own view on object-oriented methods. Although our experiences confirmed the claims about the benefits of object-oriented methods, we identified a number of important obstacles that are not addressed by current methods. This paper summarizes these obstacles and evaluates them with respect to our pilot applications. The aim of this paper is to make software engineers aware of problems they may encounter during object-oriented development, and to inspire researchers to initiate new research activities.
Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken

There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may not reflect expression at the protein level. Here, we used liquid chromatography–tandem mass spectrometry to detect and quantify expressed levels of more than 2,400 proteins in ten different tissues of male and female chicken embryos. For comparison, transcriptome sequencing was performed in the same individuals, five of each sex. The proteomic analysis revealed that dosage compensation was incomplete, with a mean male-to-female (M:F) expression ratio of Z-linked genes of 1.32 across tissues, similar to that at the RNA level (1.29). The mean Z chromosome-to-autosome expression ratio was close to 1 in males and lower than 1 in females, consistent with partly reduced Z chromosome expression in females. Although our results exclude a general mechanism for chromosome-wide dosage compensation at translation, 30% of all proteins encoded from Z-linked genes showed a significant change in the M:F ratio compared with the corresponding ratio at the RNA level. This resulted in a pattern where some genes showed balanced expression between sexes and some close to 2-fold higher expression in males. This suggests that proteomic analyses will be necessary to reveal a more complete picture of gene regulation and sex chromosome evolution.
Radar, TV and Cellular Bands: Which Spectrum Access Techniques for Which Bands?

Opportunistic access has been considered by regulators for a number of different spectrum bands. In this paper, we discuss and qualitatively evaluate techniques used in the discovery of spectrum opportunities, also called white spaces, in the radar, TV, and cellular bands. These techniques include spectrum sensing, cooperative spectrum sensing, geolocation databases, and the use of beacons. We make the case that each of the three bands considered calls for a different set of spectrum access techniques. While TV bands are well matched to the adoption of geolocation databases, a database-assisted spectrum sensing mechanism may represent the most efficient solution to exploit the spectrum holes in radar bands. We drew this conclusion based on a multitude of factors, such as the radar antennas' constant motion, and the absence of a hidden node problems in these bands. The unpredictability of cellular systems, on the other hand, calls for a more coordinated spectrum access approach, namely beacon signaling, that could be implemented using the already established cellular infrastructure and spare bits of its logical channels.
A MEMS Microphone Using Repulsive Force Sensors

We present a MEMS microphone that converts the mechanical motion of a diaphragm, generated by acoustic waves, to an electrical output voltage by capacitive fingers. The sensitivity of a microphone is one of the most important properties of its design. The sensitivity is proportional to the applied bias voltage. However, it is limited by the pull-in voltage, which causes the parallel plates to collapse and prevents the device from functioning properly. The presented MEMS microphone is biased by repulsive force instead of attractive force to avoid pull-in instability. A unit module of the repulsive force sensor consists of a grounded moving finger directly above a grounded fixed finger placed between two horizontally seperated voltage fixed fingers. The moving finger experiences an asymmetric electrostatic field that generates repulsive force that pushes it away from the substrate. Because of the repulsive nature of the force, the applied voltage can be increased for better sensitivity without the risk of pull-in failure. To date, the repulsive force has been used to engage a MEMS actuator such as a micro-mirror, but we now apply it for a capacitive sensor. Using the repulsive force can revolutionize capacitive sensors in many applications because they will achieve better sensitivity. Our simulations show that the repulsive force allows us to improve the sensitivity by increasing the bias voltage. The applied voltage and the back volume of a standard microphone have stiffening effects that significantly reduce its sensitivity. We find that proper design of the back volume and ∗Address all correspondence to this author. capacitive fingers yield promising results without pull-in instability.
Influence of pre-processing in the extraction of muscle synergies during human locomotion

The extraction of muscle synergies in human locomotion may be biased by the kind of pre-processing applied to electromyographic (EMG) data. The aim of this contribution is to analyze the differences in the muscle synergies extracted using a standard pre-processing procedure and a new procedure. The new procedure is based on the selection of the muscle's principal activations (necessary actuations of the muscle to accomplish its specific biomechanical task during gait), discarding secondary activations (with an auxiliary function in motor control). EMG signals were recorded from 12 muscles of a healthy volunteer who was asked to walk, at self-selected pace, for 5 minutes. A dataset of 193 gait cycles was collected and divided into 19 epochs of 10 concatenated gait cycles. The application of the new pre-processing procedure provided 5 instead of 6 muscle synergies accurately reconstructing the original EMG data matrix, and clearer and more stable neural activation commands. The new preprocessing procedure may be easily extended to the extraction of muscle synergies in other cyclic movements, such as running, stair climbing, cyclo-ergometer exercising, and swimming.
Facing Openness with Socio-Cognitive Trust and Categories

Typical solutions for agents assessing trust relies on the circulation of information on the individual level, i.e. reputational images, subjective experiences, statistical analysis, etc. This work presents an alternative approach, inspired to the cognitive heuristics enabling humans to reason at a categorial level. The approach is envisaged as a crucial ability for agents in order to: (1) estimate trustworthiness of unknown trustees based on an ascribed membership to categories; (2) learn a series of emergent relations between trustees observable properties and their effective abilities to fulfill tasks in situated conditions. On such a basis, categorization is provided to recognize signs (Manifesta) through which hidden capabilities (Kripta) can be inferred. Learning is provided to refine reasoning attitudes needed to ascribe tasks to categories. A series of architectures combining categorization abilities, individual experiences and context awareness are evaluated and compared in simulated experiments.