Miracle-dz/UniFAR-FTUs huggingface dataset:
The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes

Abstract Some human populations interbred with Neanderthals and Denisovans, resulting in substantial contributions to modern-human genomes. Therefore, it is now possible to use genomic data to investigate mechanisms that shaped historical gene flow between humans and our closest hominin relatives. More generally, in eukaryotes, mitonuclear interactions have been argued to play a disproportionate role in generating reproductive isolation. There is no evidence of mtDNA introgression into modern human populations, which means that all introgressed nuclear alleles from archaic hominins must function on a modern-human mitochondrial background. Therefore, mitonuclear interactions are also potentially relevant to hominin evolution. We performed a detailed accounting of mtDNA divergence among hominin lineages and used population-genomic data to test the hypothesis that mitonuclear incompatibilities have preferentially restricted the introgression of nuclear genes with mitochondrial functions. We found a small but significant underrepresentation of introgressed Neanderthal alleles at such nuclear loci. Structural analyses of mitochondrial enzyme complexes revealed that these effects are unlikely to be mediated by physically interacting sites in mitochondrial and nuclear gene products. We did not detect any underrepresentation of introgressed Denisovan alleles at mitochondrial-targeted loci, but this may reflect reduced power because locus-specific estimates of Denisovan introgression are more conservative. Overall, we conclude that genes involved in mitochondrial function may have been subject to distinct selection pressures during the history of introgression from archaic hominins but that mitonuclear incompatibilities have had, at most, a small role in shaping genome-wide introgression patterns, perhaps because of limited functional divergence in mtDNA and interacting nuclear genes.
Results from a pediatric vision screening and its ability to predict academic performance.

BACKGROUND Children attending three New York City public schools were screened in 1998-1999. These three schools were previously screened in 1996-1997. This allowed comparison of referral rates between the two years. In addition, we were able to follow individual children who attended the schools between these two years. Finally, using results of the citywide achievement test scores, we were able to correlate the specific vision screening tests with academic performance. METHODS Results from each of the years were analyzed to determine if any trend existed in referral frequency and screening procedures failed. Referral criteria were failure on one or more of the screening battery tests. In addition, the children's vision screening performance was compared with their reading achievement test scores. Vision screening results of children in both the top 25% and bottom 25% of the class were evaluated and academic improvement based on optometric intervention was also monitored. RESULTS Twenty-nine percent (29%) of children screened in 1996-1997 were referred. This matched the 25% referral rate found in 1998-1999. The screenings in 1998-1999 yielded a higher referral rate (35%) in functional vision tests as opposed to visual acuity screening procedures than the screening in 1996-1997 (30%). The King Devick Eye Movement Test and the hyperopia assessment screening showed significant correlation with citywide achievement test scores. Both these tests were significant for predicting those students in the lower 25% of the class for all grades in both years of the screenings. CONCLUSIONS Early detection and remediation increased the potential for more effective learning in a small sample size of 25 children. Further studies involving larger sample sizes are indicated.
Morphological plasticity of astroglia: Understanding synaptic microenvironment

Memory formation in the brain is thought to rely on the remodeling of synaptic connections which eventually results in neural network rewiring. This remodeling is likely to involve ultrathin astroglial protrusions which often occur in the immediate vicinity of excitatory synapses. The phenomenology, cellular mechanisms, and causal relationships of such astroglial restructuring remain, however, poorly understood. This is in large part because monitoring and probing of the underpinning molecular machinery on the scale of nanoscopic astroglial compartments remains a challenge. Here we briefly summarize the current knowledge regarding the cellular organisation of astroglia in the synaptic microenvironment and discuss molecular mechanisms potentially involved in use‐dependent astroglial morphogenesis. We also discuss recent observations concerning morphological astroglial plasticity, the respective monitoring methods, and some of the newly emerging techniques that might help with conceptual advances in the area. GLIA 2015;63:2133–2151
Wavelet spectra of nitrous oxide emission from hummocky terrain during spring snowmelt

Soil N 2 O emission data is typically highly skewed. In terrain where the spatial distribution of soil processes is controlled by topography, extreme N 2 O flux events can be highly localized and nonstationary. Wavelet analysis can be used to describe the spatial variation of these nonstationary processes. The objectives of this study were to use wavelet analysis to determine the spatial variation, scales of variability and their change over the snowmelt period for soil N 2 O flux. On a hummocky, agricultural landscape in the Dark Brown soil zone of Saskatchewan, N 2 O flux measurements were taken from a 128-point linear transect five times over the spring snowmelt season of 2004. Localized variance was determined using a continuous wavelet transform (Mexican Hat) and the local spectrum was compared with the distribution of fluxes along the transect and the relative elevation. Two spatial patterns of soil N 2 O emission were revealed. The first was a cyclic, landscape-element-controlled pattern with a scale of variation that ranged between 20 and 60 m. Changes in the spatial scale were due to a shift in importance between landscape elements as sources of peak N 2 O flux. The second pattern was composed of noncyclic, localized features that were due to extreme flux events at specific landscape positions. These extreme flux events were not temporally persistent, but represent a large, non-random contribution to mean and variance on the dates they occurred. Sample strategies to capture the full range of soil N 2 O emission at this site would probably require separate approaches for these two spatial patterns.
Laboratory experiment, field and remotely sensed data analysis for the assessment of suspended solids concentration and secchi depth of the reservoir surface water

A laboratory experiment was conducted to determine the spectral characteristics of different types of sediment under suspension in water and to select an optimal wavelength for the quantification of suspended sediment concentration and secchi depth (water clarity) in the Tawa reservoir, using the Indian Remote Sensing Satellite-1A Linear Imaging Self Scanning Scanner-I (IRS-1A LISS-I) data. It was noted that the correlation between suspended sediment concentration and reflected radiance varied with colour, mineral composition of sediment and grain size. The clay minerals of low specific gravity had a larger value of reflected radiance than those from high specific gravity non-clay minerals. The laboratory results indicated that an algorithm to quantify suspended sediment concentration and secchi depth in the reservoir can be developed from reflected radiance received by the satellite. For this purpose the Tawa reservoir on the Tawa river of the Narmada basin in Central India was selected. Tawa reservoir w.
Linguistic Cues for Distinguishing Literal and Non-Literal Usages

We investigate the effectiveness of different linguistic cues for distinguishing literal and non-literal usages of potentially idiomatic expressions. We focus specifically on features that generalize across different target expressions. While idioms on the whole are frequent, instances of each particular expression can be relatively infrequent and it will often not be feasible to extract and annotate a sufficient number of examples for each expression one might want to disambiguate. We experimented with a number of different features and found that features encoding lexical cohesion as well as some syntactic features can generalize well across idioms.
Altered thalamocortical functional connectivity in idiopathic generalized epilepsy

Aberrant thalamocortical network has been hypothesized to play a crucial role in the fundamental pathogenesis underlying idiopathic generalized epilepsy (IGE). We aimed to investigate alterations of thalamocortical functional network in patients with IGE using thalamic seed‐based functional connectivity (FC) analysis, and their relationships with frontal cognitive functions and clinical characteristics.
Skeletal muscle involvement in cardiomyopathies

The link between heart and skeletal muscle disorders is based on similar molecular, anatomical and clinical features, which are shared by the ‘primary’ cardiomyopathies and ‘primary’ neuromuscular disorders. There are, however, some peculiarities that are typical of cardiac and skeletal muscle disorders. Skeletal muscle weakness presenting at any age may indicate a primary neuromuscular disorder (associated with creatine kinase elevation as in dystrophinopathies), a mitochondrial disease (particularly if encephalopathy, ocular myopathy, retinitis, neurosensorineural deafness, lactic acidosis are present), a storage disorder (progressive exercise intolerance, cognitive impairment and retinitis pigmentosa, as in Danon disease), or metabolic disorders (hypoglycaemia, metabolic acidosis, hyperammonaemia or other specific biochemical abnormalities). In such patients, skeletal muscle weakness usually precedes the cardiomyopathy and dominates the clinical picture. Nevertheless, skeletal involvement may be subtle, and the first clinical manifestation of a neuromuscular disorder may be the occurrence of heart failure, conduction disorders or ventricular arrhythmias due to cardiomyopathy. ECG and echocardiogram, and eventually, a more detailed cardiovascular evaluation may be required to identify early cardiac involvement. Paediatric and adult cardiologists should be proactive in screening for neuromuscular and related disorders to enable diagnosis in probands and evaluation of families with a focus on the identification of those at risk of cardiac arrhythmia and emboli who may require specific prophylactic treatments, for example, pacemaker, implantable cardioverter-defibrillator and anticoagulation.
Open source software for electric field Monte Carlo simulation of coherent backscattering in biological media containing birefringence

Abstract. We present an open source electric field tracking Monte Carlo program to model backscattering in biological media containing birefringence, with computation of the coherent backscattering phenomenon as an example. These simulations enable the modeling of tissue scattering as a statistically homogeneous continuous random media under the Whittle-Matérn model, which includes the Henyey-Greenstein phase function as a special case, or as a composition of discrete spherical scatterers under Mie theory. The calculation of the amplitude scattering matrix for the above two cases as well as the implementation of birefringence using the Jones N-matrix formalism is presented. For ease of operator use and data processing, our simulation incorporates a graphical user interface written in MATLAB to interact with the underlying C code. Additionally, an increase in computational speed is achieved through implementation of message passing interface and the semi-analytical approach. Finally, we provide demonstrations of the results of our simulation for purely scattering media and scattering media containing linear birefringence.
Influence of springtime weather systems on vertical ozone distributions over three North American sites

The Atmosphere/Ocean Chemistry Experiment (AEROCE) '96 Springtime Intensive was designed to quantify major atmospheric chemical species transported from the United States east coast to the North Atlantic Ocean. During the study ozonesondes were launched almost every day between March 22 and May 3, 1996, from Charlottesville, Virginia; Purdue University, Indiana; and Bermuda. Whenever possible, the Charlottesville sondes were timed to fly behind passing cold fronts into midtropospheric to upper tropospheric bands of dry air. The dry air was hypothesized to contain ozone of stratospheric origin and was detected with color-enhanced satellite water vapor imagery. Soundings were placed in three categories: sondes launched ahead of an approaching cold front, sondes launched behind a passing cold front, and sondes launched into cutoff lows. This stratification explained much of the vertical ozone variation at each site. Tropospheric mean ozone increased with height at all three sites under postfrontal conditions, with relatively little increase with height under prefrontal conditions. Backward trajectories from Charlottesville indicated that the postfrontal air masses originated at high elevations to the northwest, while prefrontal air masses came from relatively lower elevations to the southwest. Transport also explained the lower tropospheric ozone differences between Charlottesville and Bermuda. The enhanced ozone observed in the upper troposphere over Charlottesville compared with the other sites may be linked to upwind conditions more favorable for tropopause folding. However, we believe that selective launching based on the operational use of satellite water vapor imagery allowed us to sample the full range of tropospheric ozone over Charlottesville.
Structural basis of RND-type multidrug exporters

Bacterial multidrug exporters are intrinsic membrane transporters that act as cellular self-defense mechanism. The most notable characteristics of multidrug exporters is that they export a wide range of drugs and toxic compounds. The overexpression of these exporters causes multidrug resistance. Multidrug-resistant pathogens have become a serious problem in modern chemotherapy. Over the past decade, investigations into the structure of bacterial multidrug exporters have revealed the multidrug recognition and export mechanisms. In this review, we primarily discuss RND-type multidrug exporters particularly AcrAB-TolC, major drug exporter in Gram-negative bacteria. RND-type drug exporters are tripartite complexes comprising a cell membrane transporter, an outer membrane channel and an adaptor protein. Cell membrane transporters and outer membrane channels are homo-trimers; however, there is no consensus on the number of adaptor proteins in these tripartite complexes. The three monomers of a cell membrane transporter have varying conformations (access, binding, and extrusion) during transport. Drugs are exported following an ordered conformational change in these three monomers, through a functional rotation mechanism coupled with the proton relay cycle in ion pairs, which is driven by proton translocation. Multidrug recognition is based on a multisite drug-binding mechanism, in which two voluminous multidrug-binding pockets in cell membrane exporters recognize a wide range of substrates as a result of permutations at numerous binding sites that are specific for the partial structures of substrate molecules. The voluminous multidrug-binding pocket may have numerous binding sites even for a single substrate, suggesting that substrates may move between binding sites during transport, an idea named as multisite-drug-oscillation hypothesis. This hypothesis is consistent with the apparently broad substrate specificity of cell membrane exporters and their highly efficient ejection of drugs from the cell. Substrates are transported through dual multidrug-binding pockets via the peristaltic motion of the substrate translocation channel. Although there are no clinically available inhibitors of bacterial multidrug exporters, efforts to develop inhibitors based on structural information are underway.
User Selection Algorithms for Block Diagonalization Aided Multiuser Downlink mm-Wave Communication

In order to meet the ever increasing data rate demands, the next generation of wireless communication systems is being designed for exploiting the large amounts of unused spectrum in the millimeter-wave (mm-wave) band. Since operating at mm-wave frequencies imposes several challenges, such as high-path loss, as well as both spatial and temporal channel sparsity, there is a significant research interest focused on designing feasible solutions for establishing reliable and high-throughput links at mm-wave frequencies. In this paper, we consider a cellular system relying on hybrid beamforming aided base station (BS) as well as user equipment and study the user selection problem, which has not been hitherto studied in the literature. More specifically, we study the problem of selecting $K^\prime $ -users by the BS for communication out of $K$ -users whilst ensuring that the sum rate is maximized. Specifically, we propose a user selection algorithm, which relies on the knowledge of both the channel gains and the angle of departure (AoD) of the channel paths spanning to the various users, which is termed the AoD aided user selection (AoD-US). Furthermore, we devise a pair of subspace metrics based on: 1) the angle between the subspaces spanned by the BS array response vectors; 2) the ratio of interference and signal space dimensions of various users, in order to reduce the user search space in AoD-US. This modified user selection algorithm is termed the AoD aided user selection with user set pruning (AoD-US-P). Furthermore, we study the attainable sum-rate performance of the block-diagonalization aided downlink and show that the proposed selection algorithms guarantee both multiuser diversity and multiplexing gains. Additionally, the proposed algorithms are studied in the round-robin scheduling scenario, where all the $K$ -users are scheduled for achieving fairness. Our simulation results revealed that the AoD-US-P achieves nearly the same performance as that achieved by the AoD-US despite having a small user set, while both are observed to outperform the channel power-based selection scheme.
Routing Techniques for Reliable Wireless Sensor Networks

Wireless Sensor Network (WSN) is a collection of thousands of tiny sensor nodes having capability of wireless communication, limited computation and sensing. It is now used in many application including military, environmental, healthcare application, home automation and traffic control. In this paper we will compare Data centric routing protocols for wireless sensor network. It also discusses about simulation based study of routing protocols such as Flooding and Directed Diffusion.
Dynamical and chemical effects of melting a heterogeneous source

The geochemical variability of mantle-derived melts in both trace element and isotope ratios is such as to require a chemically heterogeneous source. This raises the need to understand the dynamics of melt segregation from a heterogeneous source and the associated effects of chemical fractionation and transport. A series of idealized numerical model problems, based on a two-phase flow representation of a partially molten source region, are used to address how the physical and geochemical properties of local heterogeneities contribute to the overall segregating melts. We find that when the heterogeneities represent material that melts more easily than the background depleted mantle they will give rise to discrete traveling pulses of high melt fraction that can be understood in terms of two-dimensional solitary waves, which we separately show are solutions to the governing equations used. The generation of solitary wave-like pulses by heterogeneous melting depends on the scale of the melting anomaly compared to the natural compaction length of the partially molten system, being most effective when the region of excess melting is large. In terms of the geochemical transport by solitary waves we find that they leave behind any distinctive trace element concentration associated with the region of more rapid melting that produces the wave and therefore that the physical and chemical effects decouple. The chemical transport of incompatible trace elements by solitary waves is still anomalous in the sense that while the trace element concentration becomes no different than that of the lower melt fraction background there is locally much more of the enriched fluid (melt) moving with a large phase velocity. The general conclusion is that when a heterogeneous source partially melts it can give rise to fast moving melt fraction pulses or solitary waves, but these do not carry with them any chemical distinctiveness of the local heterogeneities that produce them. This suggests that the geochemical properties of mantle-derived melts should be interpreted in terms of averages over length scales comparable to the region of partial melting, and not particularly biased by local anomalous components even when these are preferentially melted during upwelling.
Agrobacterium-Mediated Gene Transfer to Cereal Crop Plants: Current Protocols for Barley, Wheat, Triticale, and Maize

The development of powerful “omics” technologies has enabled researchers to identify many genes of interest for which comprehensive functional analyses are highly desirable. However, the production of lines which ectopically express recombinant genes, or those in which endogenous genes are knocked down via stable transformation, remains a major bottleneck for the association between genetics and gene function in monocotyledonous crops. Methods of effective DNA transfer into regenerable cells of immature embryos from cereals by means of Agrobacterium tumefaciens have been modified in a stepwise manner. The effect of particular improvement measures has often not been significantly evident, whereas their combined implementation has resulted in meaningful advances. Here, we provide updated protocols for the Agrobacterium-mediated generation of stably transgenic barley, wheat, triticale and maize. Based upon these methods, several hundred independent transgenic lines have been delivered, with efficiencies of inoculated embryos leading to stably transgenic plants reaching 86% in barley, 10% in wheat, 4% in triticale, and 24% in maize.