Miracle-dz/UniFAR-FTUs huggingface dataset:
Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe

North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans.
Rapid Forgetting Prevented by Retrospective Attention Cues

Recent studies have demonstrated that memory performance can be enhanced by a cue which indicates the item most likely to be subsequently probed, even when that cue is delivered seconds after a stimulus array is extinguished. Although such retro-cuing has attracted considerable interest, the mechanisms underlying it remain unclear. Here, we tested the hypothesis that retro-cues might protect an item from degradation over time. We employed two techniques that previously have not been deployed in retro-cuing tasks. First, we used a sensitive, continuous scale for reporting the orientation of a memorized item, rather than binary measures (change or no change) typically used in previous studies. Second, to investigate the stability of memory across time, we also systematically varied the duration between the retro-cue and report. Although accuracy of reporting uncued objects rapidly declined over short intervals, retro-cued items were significantly more stable, showing negligible decline in accuracy across time and protection from forgetting. Retro-cuing an object’s color was just as advantageous as spatial retro-cues. These findings demonstrate that during maintenance, even when items are no longer visible, attention resources can be selectively redeployed to protect the accuracy with which a cued item can be recalled over time, but with a corresponding cost in recall for uncued items.
Energy-Efficient Joint Resource Allocation and Power Control for D2D Communications

In this paper, joint resource allocation and power control for energy-efficient device-to-device (D2D) communications underlaying cellular networks are investigated. The resource and power are optimized for maximization of the energy efficiency (EE) of D2D communications. Exploiting the properties of fractional programming, we transform the original nonconvex optimization problem in fractional form into an equivalent optimization problem in subtractive form. Then, an efficient iterative resource allocation and power control scheme is proposed. In each iteration, part of the constraints of the EE optimization problem are removed by exploiting the penalty function approach. We further propose a novel two-layer approach, which allows finding the optimum at each iteration by decoupling the EE optimization problem of joint resource allocation and power control into two separate steps. In the first layer, the optimal power values are obtained by solving a series of maximization problems through root finding, with or without considering the loss of cellular users' rates. In the second layer, the formulated optimization problem belongs to a classical resource-allocation problem with single allocation format, which admits a network flow formulation so that it can be solved to optimality. Simulation results demonstrate the remarkable improvements in terms of EE by using the proposed iterative resource allocation and power control scheme.
Microbiology and physico-chemical analysis of different sources of drinking water in Dahanu Taluka of Thane district

The present research work is an attempt to investigate quality of different sources of drinking water in Dahanu taluka of Thane district, which covered the physico-chemical, microbiological parameters and the effect of contaminated water as related to human health. Due to illiteracy and various human activities the quality of drinking water in this area is likely to change and it is not good indicator as regards to human health. Total 10 stations were selected for collection of water samples at different locations in and around Dahanu taluka region viz. Bordi, Gholwad, Chikhla, Borigaon, Aagwan, Ashagad, Kasa, Kosbad, Dabon and Dahanu. Municipal corporation of Dahanu facilitates drinking water in limited area, in alternate to this people keeps option as hand pumps, wells, river and dams etc. but water without treatment is very dangerous for consumption to human beings therefore it is very important to assess the quality of drinking water in Dahanu taluka of Thane district. The present investigation will generates database for drinking water quality and many water born diseases in Dahanu taluka of Thane district which will be helpful for Municipal Corporation and Health department of Dahanu taluka. Presence of bacteria in water samples is not a good indicator immediate action is needed circumvent this problem and necessary antimicrobial disinfectants should be employed in an important water sources.
Precursor and product processing in the bag cell neurons of Aplysia californica

Posttranslational processing in the biosynthesis of the egg-laying hormone (ELH) by the bag cell neurons of Aplysia californica was studied. The precursor (pro-ELH) to ELH was found to be resistant to solubilization in denaturant-free media throughout its lifetime. Its principle products show a similar insolubility for 3 h, but two of these, ca. 6,000 daltons, subsequently become readily recoverable in the low-speed supernatant of a homogenate of the cells. The remaining product shows no change in solubility characteristics. From studies employing ultracentrifugation and examination of axoplasmic transport, the solubility shift for the lower molecular weight products is interpreted to represent the liberation of secretory vesicles into the cytoplasm from larger membranous associations. This event is accompanied by, but does appear to be dependent upon, a 15% reduction in the molecular weight of one of the products. These findings are considered in the light of the extensively studied posttranslational processing regimen for the production of insulin in the pancreatic beta cell.
Research on the Relationship between Higher Educational Investment and Economic Growth in Hebei Province based on the Comparative Analysis of Beijing-Tianjin-Hebei

Firstly, the paper analyzes the expenditures of higher education and regional GDP in Beijing, Tianjin and Hebei from 1999 to 2016, and concludes that the educational expenditures of ordinary colleges and universities have a positive impact on the regional GDP. But in Hebei Province, the impact on the regional GDP is less effective than that in Beijing and Tianjin. Then a comparative analysis on the development level of higher education in Beijing, Tianjin and Hebei shows that Hebei is obviously behind Beijing and Tianjin. Finally, the paper gives some suggestions, such as continuing increasing investment in higher education in Hebei Province, improving the quality of higher education and achieving connotative development.
Role of radiation therapy for ‘juvenile’ angiofibroma

Abstract Juvenile nasopharyngeal angiofibroma (JNA) is a rare benign neoplasm which occurs primarily in male adolescents and is characterized by aggressive local growth. The controversy concerning appropriate treatment for patients with juvenile angiofibroma persists. Radiation therapy and surgical resection have both been reported to be effective to control a high proportion of these tumours. The case reported here demonstrates a locally advanced JNA controlled by radiation therapy.
MuSiC: Identifying mutational significance in cancer genomes

Massively parallel sequencing technology and the associated rapidly decreasing sequencing costs have enabled systemic analyses of somatic mutations in large cohorts of cancer cases. Here we introduce a comprehensive mutational analysis pipeline that uses standardized sequence-based inputs along with multiple types of clinical data to establish correlations among mutation sites, affected genes and pathways, and to ultimately separate the commonly abundant passenger mutations from the truly significant events. In other words, we aim to determine the Mutational Significance in Cancer (MuSiC) for these large data sets. The integration of analytical operations in the MuSiC framework is widely applicable to a broad set of tumor types and offers the benefits of automation as well as standardization. Herein, we describe the computational structure and statistical underpinnings of the MuSiC pipeline and demonstrate its performance using 316 ovarian cancer samples from the TCGA ovarian cancer project. MuSiC correctly confirms many expected results, and identifies several potentially novel avenues for discovery.
The Hydrophobic Core of Twin-Arginine Signal Sequences Orchestrates Specific Binding to Tat-Pathway Related Chaperones

Redox enzyme maturation proteins (REMPs) bind pre-proteins destined for translocation across the bacterial cytoplasmic membrane via the twin-arginine translocation system and enable the enzymatic incorporation of complex cofactors. Most REMPs recognize one specific pre-protein. The recognition site usually resides in the N-terminal signal sequence. REMP binding protects signal peptides against degradation by proteases. REMPs are also believed to prevent binding of immature pre-proteins to the translocon. The main aim of this work was to better understand the interaction between REMPs and substrate signal sequences. Two REMPs were investigated: DmsD (specific for dimethylsulfoxide reductase, DmsA) and TorD (specific for trimethylamine N-oxide reductase, TorA). Green fluorescent protein (GFP) was genetically fused behind the signal sequences of TorA and DmsA. This ensures native behavior of the respective signal sequence and excludes any effects mediated by the mature domain of the pre-protein. Surface plasmon resonance analysis revealed that these chimeric pre-proteins specifically bind to the cognate REMP. Furthermore, the region of the signal sequence that is responsible for specific binding to the corresponding REMP was identified by creating region-swapped chimeric signal sequences, containing parts of both the TorA and DmsA signal sequences. Surprisingly, specificity is not encoded in the highly variable positively charged N-terminal region of the signal sequence, but in the more similar hydrophobic C-terminal parts. Interestingly, binding of DmsD to its model substrate reduced membrane binding of the pre-protein. This property could link REMP-signal peptide binding to its reported proofreading function.
INFLUENCE OF THE INTRA-OCULAR PRESSURE ON THE FORMATION OF THE AQUEOUS HUMOUR AND THE OUTFLOW RESISTANCE IN THE LIVING EYE*

THIS study deals with the problem of the regulation of the intra-ocular pressure and the influence of pressure on the formation and the resistance to outflow of the aqueous humour. The main experimental approach has been to analyse the relationship between the steady state intra-ocular pressure and varied rates of flow of fluid through the anterior chamber of living and dead eyes. In the experiments on living animals, the normal rate of flow of aqueous humour was augmented by infusions of fluid directly into the anterior chamber. Provided that the factors determining the normal intraocular pressure remain constant, it is evident that the equilibrium pressure in the eye will increase proportionately with the rate at which fluid is infused into the eye. In the experiments to be described. a linear relationship was found in dead eyes over a wide range of pressures but not in eyes of living animals. The results of these studies were consistent with a Qoncept of homeostatic reflex activity in the eye which acted to minimize changes in the intra-ocular pressure, by altering either aqueous humour formation or the outflow resistance. This possibility was examined in further experiments in which the normal intra-ocular pressure and dynamics were modified experimentally. These included procedures for decreasing the rate of aqueous humour formation and the outflow resistance, and experiments in which either the nervous or the vascular supply to the eye was altered. Recently, the problem of the influence of pressure on aqueous humour dynamics has taken on additional significance following the introduction oftonography (Grant, 1950, 1951) for the measurement of the outflow facility and aqueous humour formation. This technique has been widely used in experimental and clinical studies, and its validity rests on the assumption that a moderate increase in intra-ocular pressure (10 to 15 mm. Hg) does not
Fuzzing and delta-debugging SMT solvers

SMT solvers are widely used as core engines in many applications. Therefore, robustness and correctness are essential criteria. Current testing techniques used by developers of SMT solvers do not satisfy the high demand for correct and robust solvers, as our testing experiments show. To improve this situation, we propose to complement traditional testing techniques with grammar-based blackbox fuzz testing, combined with delta-debugging. We demonstrate the effectiveness of our approach and report on critical bugs and incorrect results which we found in current state-of-the-art SMT solvers for bit-vectors and arrays.
Comparative Study of the Three Models (ANN-PMC), (DWT-ANN-PMC) and (MLR) for Prediction of the Groundwater Level of the Surface Water Table in the Saïss Plain (North of Morocco)

A new method based on the coupling of discrete wavelets (DWT) and artificial neural networks with perceptron multilayers (ANN-PMC) is proposed to predict the groundwater level. The relative performance of the DWT-ANN-PMC model has been regularly compared to artificial neural network (ANN-PMC) and multiple linear regression (MLR) models. Precipitation, temperature and average groundwater level are the variables introduced to explain and validate the models, with a monthly time step for the period March 1980 to March 2014 at two sites in the Plain of Saïss. The results of the study indicate the potential of DWT-ANN-PMC models in the prediction of groundwater levels. The forecast results indicate that the coupled wavelet neural network (WN) models were the best models for forecasting SPI values over multiple lead times in the Saïss Plain. It is recommended that further studies should explore this proposed methodology, which may in turn be used to facilitate the development and implementation of more effective strategies for the sustainable management of groundwater.
Automatic detection of mild cognitive impairment from spontaneous speech using ASR

Mild Cognitive Impairment (MCI), sometimes regarded as a prodromal stage of Alzheimer’s disease, is a mental disorder that is difficult to diagnose. However, recent studies reported that MCI causes slight changes in the speech of the patient. Our starting point here is a study that found acoustic correlates of MCI, but extracted the proposed features manually. Here, we automate the extraction of the features by applying automatic speech recognition (ASR). Unlike earlier authors, we use ASR to extract only a phonetic level segmentation and annotation. While the phonetic output allows the calculation of features like the speech rate, it avoids the problems caused by the agrammatical speech frequently produced by the targeted patient group. Furthermore, as hesitation is the most important indicator of MCI, we take special care when handling filled pauses, which usually correspond to hesitation. Using the ASR-based features, we employ machine learning methods to separate the subjects with MCI from the control group. The classification results obtained with ASR-based feature extraction are just slightly worse that those got with the manual method. The F1 value achieved (85.3) is very promising regarding the creation of an automated MCI screening application.
Visual cortex in aging and Alzheimer's disease: changes in visual field maps and population receptive fields

Although several studies have suggested that cortical alterations underlie such age-related visual deficits as decreased acuity, little is known about what changes actually occur in visual cortex during healthy aging. Two recent studies showed changes in primary visual cortex (V1) during normal aging; however, no studies have characterized the effects of aging on visual cortex beyond V1, important measurements both for understanding the aging process and for comparison to changes in age-related diseases. Similarly, there is almost no information about changes in visual cortex in Alzheimer's disease (AD), the most common form of dementia. Because visual deficits are often reported as one of the first symptoms of AD, measurements of such changes in the visual cortex of AD patients might improve our understanding of how the visual system is affected by neurodegeneration as well as aid early detection, accurate diagnosis and timely treatment of AD. Here we use fMRI to first compare the visual field map (VFM) organization and population receptive fields (pRFs) between young adults and healthy aging subjects for occipital VFMs V1, V2, V3, and hV4. Healthy aging subjects do not show major VFM organizational deficits, but do have reduced surface area and increased pRF sizes in the foveal representations of V1, V2, and hV4 relative to healthy young control subjects. These measurements are consistent with behavioral deficits seen in healthy aging. We then demonstrate the feasibility and first characterization of these measurements in two patients with mild AD, which reveal potential changes in visual cortex as part of the pathophysiology of AD. Our data aid in our understanding of the changes in the visual processing pathways in normal aging and provide the foundation for future research into earlier and more definitive detection of AD.
Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400

The DNA region encoding biphenyl dioxygenase, the first enzyme in the biphenyl-polychlorinated biphenyl degradation pathway of Pseudomonas species strain LB400, was sequenced. Six open reading frames were identified, four of which are homologous to the components of toluene dioxygenase from Pseudomonas putida F1 and have been named bphA, bphE, bphF, and bphG. From this comparison, biphenyl dioxygenase was found to be a multicomponent enzyme containing a two-subunit iron-sulfur protein, a ferredoxin, and a reductase. Comparison of the large subunit of the iron-sulfur protein and the ferredoxin with other multicomponent dioxygenases identified amino acid sequences similar to Rieske iron-sulfur proteins for binding a [2Fe-2S] cluster. Sequences have also been identified in the reductase component that match the consensus sequence for FAD or NAD binding. Transcription of the biphenyl dioxygenase region was examined, and three transcription initiation sites were identified. Transcription initiating at the site furthest upstream is greatly increased when the LB400 cells are grown on biphenyl as the sole carbon source.
Architectonic Subdivisions of Neocortex in the Gray Squirrel (Sciurus carolinensis)

Squirrels are highly visual mammals with an expanded cortical visual system and a number of well‐differentiated architectonic fields. To describe and delimit cortical fields, subdivisions of cortex were reconstructed from serial brain sections cut in the coronal, sagittal, or horizontal planes. Architectonic characteristics of cortical areas were visualized after brain sections were processed with immunohistochemical and histochemical procedures for revealing parvalbumin, calbindin, neurofilament protein, vesicle glutamate transporter 2, limbic‐associated membrane protein, synaptic zinc, cytochrome oxidase, myelin or Nissl substance. In general, these different procedures revealed similar boundaries between areas, suggesting that functionally relevant borders were being detected. The results allowed a more precise demarcation of previously identified areas as well as the identification of areas that had not been previously described. Primary sensory cortical areas were characterized by sparse zinc staining of layer 4, as thalamocortical terminations lack zinc, as well as by layer 4 terminations rich in parvalbumin and vesicle glutamate transporter 2. Primary areas also expressed higher levels of cytochrome oxidase and myelin. Primary motor cortex was associated with large SMI‐32 labeled pyramidal cells in layers 3 and 5. Our proposed organization of cortex in gray squirrels includes both similarities and differences to the proposed of cortex in other rodents such as mice and rats. The presence of a number of well‐differentiated cortical areas in squirrels may serve as a guide to the identification of homologous fields in other rodents, as well as a useful guide in further studies of cortical organization and function. Anat Rec, 291:1301–1333, 2008. © 2008 Wiley‐Liss, Inc.