Miracle-dz/UniFAR-FTUs huggingface dataset:
GC composition of the human genome: in search of isochores.

The isochore theory, proposed nearly three decades ago, depicts the mammalian genome as a mosaic of long, fairly homogeneous genomic regions that are characterized by their guanine and cytosine (GC) content. The human genome, for instance, was claimed to consist of five distinct isochore families: L1, L2, H1, H2, and H3, with GC contents of <37%, 37%-42%, 42%-47%, 47%-52%, and >52%, respectively. In this paper, we address the question of the validity of the isochore theory through a rigorous sequence-based analysis of the human genome. Toward this end, we adopt a set of six attributes that are generally claimed to characterize isochores and statistically test their veracity against the available draft sequence of the complete human genome. By the selection criteria used in this study: distinctiveness, homogeneity, and minimal length of 300 kb, we identify 1,857 genomic segments that warrant the label "isochore. " These putative isochores are nonuniformly scattered throughout the genome and cover about 41% of the human genome. We found that a four-family model of putative isochores is the most parsimonious multi-Gaussian model that can be fitted to the empirical data. These families, however, are GC poor, with mean GC contents of 35%, 38%, 41%, and 48% and do not resemble the five isochore families in the literature. Moreover, due to large overlaps among the families, it is impossible to classify genomic segments into isochore families reliably, according to compositional properties alone. These findings undermine the utility of the isochore theory and seem to indicate that the theory may have reached the limits of its usefulness as a description of genomic compositional structures.
Effect of pH on Isolation and Distribution of Members of Subdivision 1 of the Phylum Acidobacteria Occurring in Soil

ABSTRACT The pH strongly influenced the development of colonies by members of subdivision 1 of the phylum Acidobacteria on solid laboratory media. Significantly more colonies of this group formed at pH 5.5 than at pH 7.0. At pH 5.5, 7 to 8% of colonies that formed on plates that were incubated for 4 months were formed by subdivision 1 acidobacteria. These colonies were formed by bacteria that spanned almost the entire phylogenetic breadth of the subdivision, and there was considerable congruence between the diversity of this group as determined by the cultivation-based method and by surveying 16S rRNA genes in the same soil. Members of subdivision 1 acidobacteria therefore appear to be readily culturable. An analysis of published libraries of 16S rRNAs or 16S rRNA genes showed a very strong correlation between the abundance of subdivision 1 acidobacteria in soil bacterial communities and the soil pH. Subdivision 1 acidobacteria were most abundant in libraries from soils with pHs of <6, but rare or absent in libraries from soils with pHs of >6.5. This, together with the selective cultivation of members of the group on lower-pH media, indicates that growth of many members of subdivision 1 acidobacteria is favored by slightly to moderately acidic growth conditions.
Resource allocation and pricing mechanisms for wireless networks with malicious users

We propose a framework for designing decentralized pricing and centralized auction mechanisms without and with malicious users. We design pricing mechanism for different designer objectives such as efficient allocation, revenue maximization and energy minimization. A new modelling of malicious user utility function is proposed and a metric PoM is defined and calculated. We relax the assumption that the users and the designer know the nature of users and design Bayesian mechanisms.
Sensitivity of the ITCZ Location to Ocean Forcing Via Q‐Flux Green's Function Experiments

The sensitivity of the intertropical convergence zone (ITCZ) position to forcing patterns is important for understanding changes in tropical rainfall. A set of Green's function experiments reveals hat this sensitivity is asymmetric depending on which hemisphere (northern or southern) the forcing is applied. Northern hemisphere forcings produce a much larger response than southern hemisphere forcings of similar magnitude. The response of the ITCZ position to forcing can be broken into linear and nonlinear components, and it is shown that the asymmetry arises from the nonlinear component. The linear and nonlinear response components have similar magnitudes, but the pattern of the nonlinear component is insensitive to the location of the forcing, such that it amplifies the response to northern hemisphere forcings and dampens the response to southern hemisphere forcings. This asymmetry hints at an intrinsic mode of the climate system, depending on the current climate state.
Radiation characteristics of a novel compact microstrip patch resonator

In this paper a new type of dual-mode compact resonator for mobile communication systems, in the 900 MHz frequency band, is investigated. This compact planar resonator, developed on a 0.635 mm substrate with a 10.8 dielectric constant, has a square shape with an edge of 20.5 mm. For this dual resonator, several methods of modes coupling were considered. The radiation characteristics of this new resonator were investigated.
StorylineViz: A [Space, Time, Actors, Motion] Segmentation Method for Visual Text Exploration

Supporting knowledge discovery through visual means is a hot research topic in the field of visual analytics in general, and a key issue in the analysis of textual data sets. In that context, the StorylineViz study aims at developing a generic approach to narrative analysis, supporting the identification of significant patterns inside textual data, and ultimately knowledge discovery and sensemaking. It builds on a text segmentation procedure through which sequences of situations are extracted. A situation is defined by a quadruplet of components: actors, space, time and motion. The approach aims at facilitating visual reasoning on the structure, rhythm, patterns and variations of heterogeneous texts in order to enable comparative analysis, and to summarise how the space/time/actors/motion components are organised inside a given narrative. It encompasses issues that are rooted in Information Sciences - visual analytics, knowledge representation â and issues that more closely relate to Digital Humanities â comparative methods and analytical reasoning on textual content, support in teaching and learning, cultural mediation.
Application and Results of the AO Internal Fixation System in Nontraumatic Indications

The AO internal skeletal fixation system (ISFS) permits posterior spine fixation to be restricted to the vertebrae immediately adjacent to the lesion and allows manipulation of each instrumented vertebra in three planes. In a prospective study to assess the value of this fixation for adult spinal disorders, 68 patients were reviewed. The device was used in spondylolisthesis, postlaminectomy instability, post-traumatic kyphosis, degenerative scoliosis, spinal stenosis, tumors, and infections. A total of 322 transpedicular screws have been inserted without neurologic complication. Satisfactory results were achieved in 88% of the patients, and only four pseudarthroses (6%) occurred. The ISFS provides rigid stabilization to enhance bone graft consolidation and to allow rapid postoperative mobilization in a light external orthosis.
Point Cloud Generation from Aerial Image Data Acquired by a Quadrocopter Type Micro Unmanned Aerial Vehicle and a Digital Still Camera

The objective of this investigation was to develop and investigate methods for point cloud generation by image matching using aerial image data collected by quadrocopter type micro unmanned aerial vehicle (UAV) imaging systems. Automatic generation of high-quality, dense point clouds from digital images by image matching is a recent, cutting-edge step forward in digital photogrammetric technology. The major components of the system for point cloud generation are a UAV imaging system, an image data collection process using high image overlaps, and post-processing with image orientation and point cloud generation. Two post-processing approaches were developed: one of the methods is based on Bae Systems’ SOCET SET classical commercial photogrammetric software and another is built using Microsoft®’s Photosynth™ service available in the Internet. Empirical testing was carried out in two test areas. Photosynth processing showed that it is possible to orient the images and generate point clouds fully automatically without any a priori orientation information or interactive work. The photogrammetric processing line provided dense and accurate point clouds that followed the theoretical principles of photogrammetry, but also some artifacts were detected. The point clouds from the Photosynth processing were sparser and noisier, which is to a large extent due to the fact that the method is not optimized for dense point cloud generation. Careful photogrammetric processing with self-calibration is required to achieve the highest accuracy. Our results demonstrate the high performance potential of the approach and that with rigorous processing it is possible to reach results that are consistent with theory. We also point out several further research topics. Based on theoretical and empirical results, we give recommendations for properties of imaging sensor, data collection and processing of UAV image data to ensure accurate point cloud generation.
A Centennial Episode of Weak East Asian Summer Monsoon in the Midst of the Medieval Warming

Recent paleoproxy evidence has suggested that there is a centennial episode of weaker East Asian summer monsoon (EASM) within the Medieval Warm Period, in which the EASM is generally strong. This study aims to explore the causes of this phenomenon and determine what controls the centennial variability of the EASM. With the Community Earth System Model, a suite of control and forced experiments were conducted for the past 2,000 years. The model simulates a warm period over EA (East Asia) from CE 801–1250 with a generally increased summer mean precipitation over the northern EA; however, during CE 980–1100, the EASM is significantly weaker. On the multi‐decadal to centennial time scale, a strong EASM is associated with a La Niña‐like Indo‐Pacific warming, and a weak EASM with the El Niño‐like conditions. This sea surface temperature anomaly pattern represents the leading EOF (empirical orthogonal function) mode of centennial sea surface temperature variations, which are primarily forced by solar radiation and volcanic activity. In contrast, land use/land cover and greenhouse gases as well as internal dynamics play a negligible role. The weak EASM during CE 980–1100 is attributed to the relatively low solar radiation, which leads to a prevailing El Niño‐like Indo‐Pacific cooling with the strongest cooling occurring in the equatorial western Pacific. The suppressed convection over the equatorial western Pacific directly induces a Philippine Sea anticyclone anomaly, which increases the southern China precipitation, while suppressing Philippine Sea precipitation. The latter excites a meridional teleconnection that induces anomalous northerly winds and dry conditions over northern China.
Memory cost analysis for OpenFlow multiple table lookup

Multiple Table Lookup architectures in Software Defined Networking (SDN) open the door for exciting new network applications. The development of the OpenFlow protocol supported the SDN paradigm. However, the first version of the OpenFlow protocol specified a single table lookup model with the associated constraints in flow entry numbers and search capabilities. With the introduction of multiple table lookup in OpenFlow v1.1, flexible and efficient search to support SDN application innovation became possible. However, implementation of multiple table lookup in hardware to meet high performance requirements is non-trivial. One possible approach involves the use of multi-dimensional lookup algorithms. A high lookup performance can be achieved by using embedded memory for flow entry storage. A detailed study of OpenFlow flow filters for multi-dimensional lookup is presented in this paper. Based on a proposed multiple table lookup architecture, the memory consumption and update performance using parallel single field searches are evaluated. The results demonstrate an efficient multi-table lookup implementation with minimum memory usage.
A Nonresonant Self-Synchronizing Inductively Coupled 0.18- $\mu $ m CMOS Power Receiver and Charger

While the functionality of emerging wireless microsensors, cellular phones, and biomedical implants, to name a few, is on the rise, their dimensions continue to shrink. This is unfortunate because smaller batteries exhaust quicker. Not surprisingly, recharging batteries wirelessly is becoming increasingly popular today. Still, small pickup coils cannot harness much, so induced EMF voltages vEMF.S are low. Modern receivers can resonate these low input voltages to rectifiable levels, but only with a finely tuned capacitor that resonates at megahertz when on-chip and at kilohertz when off-chip. In other words, resonant rectifiers are sensitive to frequency and dissipate considerable switching power when integrated on-chip. Unluckily, excluding the resonant capacitor requires a control signal that synchronizes switching events to the transmitter's operating frequency. The 0.18-μm CMOS prototype presented here derives this synchronizing signal from the coupled vEMF.S by counting the number of pulses of a higher-frequency clock across a half cycle during a calibration phase and using that number to forecast half-cycle crossings. This way, the prototyped IC switches every half cycle to draw up to 557 μW from 46.6 to 585-mVPK signals with 38%-84% efficiency across 1.0-5.0 cm.
Both intrathymic and peripheral selection modulate the differential expression of V beta 5 among CD4+ and CD8+ T cells

Murine T cells expressing V beta 5 are characterized by (a) intrathymic deletion in the presence of I-E and products of endogenous mouse mammary tumor viruses, and (b) a greater representation in CD8+ relative to CD4+ peripheral T cells, thought to be due to more efficient intrathymic positive selection on class I rather than class II major histocompatibility complex antigens. We have engineered mice that are transgenic for a rearranged gene encoding a V beta 5+ beta chain of the T cell receptor for antigen. Deletion is not predicted in I-E- V beta 5+ transgenic mice, and until the age of 2 wk, the CD4/CD8 ratio of peripheral T cells is > 3:1 and indistinguishable between transgenic and nontransgenic mice. Transgenic mice then show a rapid, age-dependent decline in the ratio of CD4+ to CD8+ T cells in the lymphoid periphery, reaching a low of 1:10 by 7 mo of age. Furthermore, the percent of peripheral CD4+ cells that express the transgene drops with age, reaching a low of about 60% at 7 mo, while the percent of CD8+ cells that express V beta 5 remains greater than 95% at all ages. The lymphoid periphery is implicated in this selection against CD4+ V beta 5+ T cells as it occurs more rapidly in thymectomized transgenic mice, and can be delayed in mice whose peripheral T cells are replaced by recent thymic emigrants after depletion by in vivo treatment with anti-Thy-1 antibodies. These results indicate that the relative expression of V beta 5 in T cell subsets can be influenced not only intrathymically in I-E+ V beta 5+ transgenic mice, but also by events in the periphery, in the absence of I-E expression.
A Comparison of Approaches for Sentiment Classification on Lithuanian Internet Comments

Despite many methods that effectively solve sentiment classification task for such widely used languages as English, there is no clear answer which methods are the most suitable for the languages that are substantially different. In this paper we attempt to solve Internet comments sentiment classification task for Lithuanian, using two classification approaches – knowledge-based and supervised machine learning. We explore an influence of sentiment word dictionaries based on the different parts-of-speech (adjectives, adverbs, nouns, and verbs) for knowledge-based method; different feature types (bag-ofwords, lemmas, word n-grams, character n-grams) for machine learning methods; and pre-processing techniques (emoticons replacement with sentiment words, diacritics replacement, etc.) for both approaches. Despite that supervised machine learning methods (Support Vector Machine and Naive Bayes Multinomial) significantly outperform proposed knowledge-based method all obtained results are above baseline. The best accuracy 0.679 was achieved with Naive Bayes Multinomial and token unigrams plus bigrams, when pre-processing involved diacritics replacement.
Early origins of modern birds and mammals: molecules vs. morphology.

Recent claims from molecular evidence that modern orders of birds and mammals arose in the Early Cretaceous, over 100 million years (Myr) ago, are contrary to palaeontological evidence. The oldest fossils generally fall in the time range from 70-50 Myr ago, with no earlier finds. If the molecular results are correct, then the first half of the fossil record of modern birds and mammals is missing. Suggestions that this early history was played out in unexplored parts of the world, or that the early progenitors were obscure forms, are unlikely. Intense collecting over hundreds of years has failed to identify these missing fossils. Control experiments, in the form of numerous Cretaceous-age fossil localities which yield excellently preserved lizards, salamanders, birds, and mammals, fail to show the modern forms. The most likely explanation is that they simply did not exist, and that the molecular clock runs fast during major radiations.
Multilevel regulation of histone gene expression during the cell cycle in tobacco cells

The respective involvement of transcriptional and post-transcriptional mechanisms in coupling H3 and H4 histone gene expression to the S phase of the cell cycle has been studied in synchronized tobacco cells. Induction of histone gene expression at the G1/S transition is shown to be essentially directed by an increase in the transcription rate in response to cellular signals occurring at the initiation step of DNA replication. Histone gene induction thus precedes the burst of DNA synthesis. However, when the elongation step of DNA replication is ineffective or artificially arrested, feedback mechanisms apparently act at the translation level to avoid overproduction of histone proteins from their mRNAs. At the end of S phase, post-transcriptional mechanisms ensure a rapid degradation of histone mRNAs. Transcription factors are bound to the cis -elements of histone promoters throughout the cell cycle, thus suggesting a post-translational modification of some of them to trigger promoter activation at the G1/S transition. Based on these results, a model is proposed for histone gene transcriptional induction in connection with the components of the cell cycle machinery.
Equivalent circuit GaN HEMT model accounting for gate-lag and drain-lag transient effects

This paper introduces a full nonlinear compact equivalent circuit model (ECM) for a 10 W Gallium Nitride (GaN) high electron-mobility transistor (HEMT). The model accounts for low-frequency dispersion of both transconductance and output conductance by use of gate and drain filter networks applied to GaN for the first time. Other features of the model include an excellent fit of modelled drain-current to high-power pulsed-IV (P-IV) measurements up to 60 V across a range of quiescent points, using a single function drain-current equation. Global S-parameter fits across the bias plane have also been extracted. Large-signal harmonic sweeps are presented, showing a good fit to measured data over a range of bias points.
Decisive influence on torque ripples of permanent Magnet assisted Synchronous Motor by the carrier harmonics

In this paper, decisive influences of the carrier harmonics on torque characteristic for Permanent Magnet assisted Synchronous Reluctance Motor (PMa-SynRM), which has been purposely designed for EV drive system, is numerically investigated. In the design process of PMa-SynRM, stator skew and short pitch winding are adopted in order to reduce torque ripple causing the acoustic noise, vibration. First of all, not only the specification of the PMa-SynRM, but the reduction design process and the performance characteristics such as torque production and ripples are presented. Subsequently, the remarkable torque analysis result, that is obtained using 3-D modeling considering skewed stator structure and the carrier harmonics, is covered in priority. Meanwhile, numerical analysis of its performance is carried out with the Finite Element Method (FEM).
Non-catalytic participation of the Pin1 peptidyl-prolyl isomerase domain in target binding

Pin1 is a phosphorylation-dependent peptidyl-prolyl isomerase (PPIase) that has the potential to add an additional level of regulation within protein kinase mediated signaling pathways. Furthermore, there is a mounting body of evidence implicating Pin1 in the emergence of pathological phenotypes in neurodegeneration and cancer through the isomerization of a wide variety of substrates at peptidyl-prolyl bonds where the residue preceding proline is a phosphorylated serine or threonine residue (i.e., pS/T-P motifs). A key step in this regulatory process is the interaction of Pin-1 with its substrates. This is a complex process since Pin1 is composed of two domains, the catalytic PPIase domain, and a type IV WW domain, both of which recognize pS/T-P motifs. The observation that the WW domain exhibits considerably higher binding affinity for pS/T-P motifs has led to predictions that the two domains may have distinct roles in mediating the actions of Pin1 on its substrates. To evaluate the participation of its individual domains in target binding, we performed GST pulldowns to monitor interactions between various forms of Pin1 and mitotic phospho-proteins that revealed two classes of Pin-1 interacting proteins, differing in their requirement for residues within the PPIase domain. From these observations, we consider models for Pin1-substrate interactions and the potential functions of the different classes of Pin1 interacting proteins. We also compare sequences that are recognized by Pin1 within its individual interaction partners to investigate the underlying basis for its different types of interactions.
To Veer or Not to Veer: Learning from Experts How to Stay Within the Crosswalk

One of the many challenges faced by visually impaired (VI) individuals is the crossing of intersections while remaining within the crosswalk. We present a Learning from Demonstration (LfD) approach to tackle this problem and provide VI users with an assistive agent. Contrary to previous methods, our solution does not presume the existence of particular features in crosswalks. The application of the LfD framework helped us transfer sighted individuals' abilities to the intelligent assistive agent. Our proposed approach started from a collection of 215 demonstrative videos of intersection crossings executed by sighted individuals ("the experts"). We labeled the video frames to gather the experts' recommended actions, and then applied a policy derivation technique to extract the optimal behavior using state-of-the-art Convolutional Neural Networks. Finally, to assess the feasibility of such a solution, we evaluated the performance of the trained agent in predicting expert actions.