Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxford Nanopore Sequencing and de novo Assembly of a Eukaryotic Genome

Monitoring the progress of DNA through a pore has been postulated as a method for sequencing DNA for several decades 1,2 . Recently, a nanopore instrument, the Oxford Nanopore MinION, has become available 3 . Here we describe our sequencing of the S. cerevisiae genome. We describe software developed to make use of these data as existing packages were incapable of assembling long reads at such high error rate (~35% error). With these methods we were able to error correct and assemble the nanopore reads de novo , producing an assembly that is contiguous and accurate: with a contig N50 length of 479kb, and has greater than 99% consensus identity when compared to the reference. The assembly with the long nanopore reads was able to correctly assemble gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in an assembly using Illumina sequencing alone (with a contig N50 of only 59,927bp).
Habitat Relationships of Landbirds in the Northern Region, USDA Forest Service

Hutto, Richard L. ; Young, Jock S. 1999. Habitat relationships of landbirds in the Northern Region, USDA Forest Service. Gen. Tech. Rep. RMRS-GTR-32. Ogden, UT: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 72 p. A series of first-generation habitat-relationships models for 83 bird species were detected in a 3-year study on point counts conducted in association with the USDA Forest Service's Northern Region Landbird Monitoring Program. The models depict probabilities of detection for each of the bird species on 100-m-radius, 1 O-minute point counts conducted across a series of major vegetation cover types. Based on these models, some bird species appear to be restricted in their habitat distribution to: (1) postfire, standing-dead forests, (2) relatively uncut, older forests, (3) harvested forest types, (4) marshes, (5) riparian environments, and (6) grasslands and sagebrush. Such restricted distributions highlight the need to provide adequate amounts of these cover types to maintain viable species populations. Many bird species were relatively abundant in harvested forests, suggesting a need for nesting success studies because timber harvesting creates unnatural cover types that may elicit settling responses by species that are 'iprogrammed" to respond to similar naturally occurring cover types. Thus, these unnatural cover types could be acting as "ecological traps," where species are being attracted to sites where suitability is relatively poor. These preliminary results demonstrate the utility of a landbird monitoring program, and suggest that agencies such as the Forest Service should consider broadening the indicator species concept to monitor groups of species (such as landbirds and butterflies) that can be easily sampled with a single field method. The list of species covered by this program is indeed large enough and ecologically broad enough to help managers predict and monitor the effects of management activities on almost all the major vegetation types in the region. The detail and region-specific nature of this information can be matched by no other database in existence on landbirds, and the information should prove useful to land managers in planning areas that might consist of alternative cover types.
Implementation of a Physically Unclonable Function on an FPGA

This paper shows the implementation of a physically unclonable function (PUF) of the arbiter type and its modifications, the generation of random numbers and unique identifiers, and a statistical analysis of the generated sequences of random numbers. Within the framework of this work, experiments were carried out on different SoC, SoM crystals and within the same crystal with different placement on it, experiments with PUF modeling based on machine learning were simulated. The results and conclusions provide recommendations for the optimal and safe use of PUF.
Analysis and Design of a Tapered Stripline with a Tapered Slot for Stripline Transitions

This letter proposed to study the characteristic impedance of a tapered stripline (SL) with a tapered slot. The conformal transformation is applied to obtain the analytical formula, which provides guidance for the impedance matching of the gradual stripline transitions. To validate the accuracy of the proposed formula, the tapered SL with the tapered slot is designed under low temperature co-fired ceramic (LTCC) process. The results calculated by the proposed analytical formula agrees with the results of full wave approach very well. The relative errors between the two results are less than 4%.
Comparison of Ki67 Proliferation Index in Gastrointestinal Non-Hodgkin Large B-Cell Lymphomas: The Conventional Method of Evaluation or AI Evaluation?

The most common NHL subtype in SEEU is DLBCL (39%), and it manifests with a variety of cellular morphologies and a high proliferation index. Also, the GI tract is the most common site of extranodal NHLs, and most NHLs involving the GI tract are of B-cell lineage, of which diffuse large B-cell lymphoma is the most common subtype, irrespective of location. The last few years have seen digital pathology as a vital technology that has a positive impact on diagnostics, but studies on the use of DP for lymphoma identification, however, are still restricted to only determining whether a tumor is present or absent. Using the example of cases of malignant NHL, we aim to investigate the diagnostic utility of DP using QuPath software in evaluating the proliferation index and the prognostic significance and to show that improved visualization and analysis contribute to the convergence of these complementary diagnostic modalities for lymphomas. The average proliferation index (Ki67) was 58.33% with values between 10% and 85%. After the stratification of the cases, an increased proliferation index was observed in the majority of cases (53.33%), and this aspect was associated with the advanced age of the patients (p = 0.045). Visual assessment provides lower Ki67 values than automated digital image analysis. However, the agreement coefficient between the conventional method and the AI method indicates an excellent level of reliability (ICC1–0.970, ICC2–0.990). The multivariate analysis revealed that in the cases where the proliferation index Ki67 is high (˃70%), the IPI score represents an important risk factor predicting mortality (HR = 10.597, p = 0.033).
Multi-objective Optimization for Dynamic Service Placement Strategy for Real-Time Applications in Fog Infrastructure

Fog computing is rising as a dominant and modern computing model that thrives on delivering Internet of Things (IoT) computations. It is an addition to cloud computing, helping it handle services needing a faster response. A well-built dynamic service placement strategy could improve fog performance. This paper proposes a dynamic service placement strategy in a fog infrastructure for real-time applications. The main idea of this work is to perform a multi*objective optimization on response time and available resources in fog networks. Hence, depending on the fog node's response time and available computational resources, the algorithm will choose the fittest node to send the service in real-time. Finally, we model and evaluate our proposed strategy in the iFogSim-simulated Fog infrastructure. Results of the simulation studies demonstrate significant improvement in response time and resource utilization over several other strategies, improving the fog network's performance.
SCALR: Communication-Efficient Secure Multi-Party Logistic Regression

Privacy-preserving coded computing is a popular framework for multiple data-owners to jointly train machine learning models, with strong end-to-end information-theoretic privacy guarantees for the local data. A major challenge against the scalability of current approaches is their communication overhead, which is quadratic in the number of users. Towards addressing this challenge, we present SCALR, a communication-efficient collaborative learning framework for training logistic regression models. To do so, we introduce a novel coded computing mechanism, by decoupling the communication-intensive encoding operations from real-time training, and offloading the former to a data-independent offline phase, where the communicated variables are independent from training data. As such, the offline phase can be executed proactively during periods of low network activity. Communication complexity of the data-dependent (online) training operations is only linear in the number of users, greatly reducing the quadratic state-of-the-art. Our theoretical analysis presents the information-theoretic privacy guarantees, and shows that SCALR achieves the same performance guarantees as the state-of-the-art, in terms of adversary resilience, robustness to user dropouts, and model convergence. Through extensive experiments, we demonstrate up to $80\times $ reduction in online communication overhead, and $6\times $ speed-up in the wall-clock training time compared to the state-of-the-art.
Geocronologia e petrotrama de quartzo milonitos do duplex transcorrente de Lavras da Mangabeira

FREIMANN, M.A. Geochronology and milonites quartz fabric of the strike-slip duplex from Lavras 2014. Slices of metaplutonic rocks, banded gneiss, amphibolites and metasedimentary sequences form a strike-slip duplex situated in the west portion of the Patos Lineament (Borborema Province, Northeastern Brazil). U-Pb (LA-ICP-MS) data in zircons from the imbricate slices indicate they are constituted by rocks of different ages. Banded gneiss, orthogneisses and metaultramafic dikes assembled in the Granjeiro Complex yielded Archean ages between 2.8 and 3.2 Ga. In contrast, biotite gneisses and amphibolites produced a Siderian (ca. 2.4 Ga) age and an augen gneiss apparently intrusive in the Siderian sequences yielded a Rhyacian (ca. 2.2 Ga) age. These basement sequences are in allochtonous contact with metapelites and quartzites grouped in the Lavras da Mangabeira Formation of Neoprotrozoic age. Kinematic criteria deduced from the study of the microstructures and crystallographic fabric of quartz-rich mylonites show that the metasedimentary sequence was thrusted to the northeast direction. Crystalligraphic c- and a- axis of quartz indicated that medium- to high temperature slip-systems were active during the fabric development. Temperature estimations based on the opening-angle of the c-axis fabric and the sutured contacts between quartz-quartz grains indicated that the ductile deformation occurred at 500 and 700°C. The development of the tectonic duplex was likely facilitated by the occurrence of Archean rocks involved in the shear deformation. They would have acted as a rigid (competent) material that induce the stacking of the sequences during the bulk dextral transcurrent deformation of the Patos Lineament.
Deontic Paradoxes in ASP with Weak Constraints

The rise of powerful AI technology for a range of applications that are sensitive to legal, social, and ethical norms demands decision-making support in presence of norms and regulations. Normative reasoning is the realm of deontic logics, that are challenged by well-known benchmark problems (deontic paradoxes), and lack efficient computational tools. In this paper, we use Answer Set Programming (ASP) for addressing these shortcomings and showcase how to encode and resolve several well-known deontic paradoxes utilizing weak constraints. By abstracting and generalizing this encoding, we present a methodology for translating normative systems in ASP with weak constraints. This methodology is applied to"ethical"versions of Pac-man, where we obtain a comparable performance with related works, but ethically preferable results.
Long-term environmental enrichment is associated with better fornix microstructure in older adults

Background Sustained environmental enrichment (EE) through a variety of leisure activities may decrease the risk of developing Alzheimer’s disease. This cross-sectional cohort study investigated the association between long-term EE in young adulthood through middle life and microstructure of fiber tracts associated with the memory system in older adults. Methods N = 201 cognitively unimpaired participants (≥ 60 years of age) from the DZNE-Longitudinal Cognitive Impairment and Dementia Study (DELCODE) baseline cohort were included. Two groups of participants with higher (n = 104) or lower (n = 97) long-term EE were identified, using the self-reported frequency of diverse physical, intellectual, and social leisure activities between the ages 13 to 65. White matter (WM) microstructure was measured by fractional anisotropy (FA) and mean diffusivity (MD) in the fornix, uncinate fasciculus, and parahippocampal cingulum using diffusion tensor imaging. Long-term EE groups (lower/higher) were compared with adjustment for potential confounders, such as education, crystallized intelligence, and socio-economic status. Results Reported participation in higher long-term EE was associated with greater fornix microstructure, as indicated by higher FA (standardized β = 0.117, p = 0.033) and lower MD (β = −0.147, p = 0.015). Greater fornix microstructure was indirectly associated (FA: unstandardized B = 0.619, p = 0.038; MD: B = −0.035, p = 0.026) with better memory function through higher long-term EE. No significant effects were found for the other WM tracts. Conclusion Our findings suggest that sustained participation in a greater variety of leisure activities relates to preserved WM microstructure in the memory system in older adults. This could be facilitated by the multimodal stimulation associated with the engagement in a physically, intellectually, and socially enriched lifestyle. Longitudinal studies will be needed to support this assumption.
Prediction of brain activity response by functional magnetic resonance imaging based on semantic information

This study investigated an improved method for predicting brain activity using 7T fMRI data. The data resolution was 7T, and the stimulus and fMRI measurement data were paired. Text descriptions were used as original features and were deep learning encoded for model training. The results demonstrated that our model effectively predicted brain activity response, surpassing some previous methods. During experiments, increasing the encoding dimension improved the model's fitting performance. Our study enhances the ability to simulate the brain and investigate its cognitive processes.
Facial Emotion Level Recognition Using CNN

Humans have traditionally found it easy to determine emotions from facial expressions, but doing so using a computer algorithm is much more difficult. The ability to recognise these emotions is a key element of natural human-machine interfaces. Thus, Facial Emotion Level Recognition covers a wide range of applications. In this paper, We present a novel technique for identifying the intensity of emotions using CNN.
Oil Vulnerability in the Greater Toronto Area: Spatial Analyses of Socioeconomic Risks from Higher Urban Fuel Prices

The rising cost of fossil fuel is a recognized phenomenon, but its impact at the household level is still widely unknown. Understanding how the socioeconomic impacts of rising fuel prices might be distributed across urban areas is a critical issue that is necessary for sustainable urban transportation planning. This study has refined the vulnerability index for petrol expense rises (VIPER) framework previously proposed by Dodson and Sipe (2007) by incorporating travel survey data to better represent households’ car dependence. Through this modified VIPER framework, the authors seek to understand how the socioeconomic impact of rising fuel costs will be distributed across the Greater Toronto Area (GTA). The findings of this research reveal a pattern in the distribution of oil vulnerability that depicts a three-ring configuration: expanding outwards from the lowest oil vulnerability in the urban core (1st ring), followed by the highest oil vulnerability in the city’s inner suburbs (2nd ring), and a transition to a lower oil vulnerability in the suburban areas (3rd ring). Such results reveal the need for transportation and land use policy measures that tackle transportation-related social exclusion due to high fuel prices in the future.
A Bibliometric Analysis of Computational Social Science in Turkish Academia

Using bibliometrics, this study explores the land-scape of social computing sciences within the Turkish academic sphere. The analysis conducted at both the country and organizational levels reveals that collaborations in the field of social computing are not solely influenced by geographical factors. Through network analysis of keyword co-occurrences, distinct thematic patterns emerge, highlighting areas such as health-related applications, the social implications of computational approaches, the intersection of computational methods with the economy and agriculture, machine learning techniques, and the utilization of big data analytics for business applications. These findings provide evidence of the multidisciplinary nature inherent in social computing research.
Crystal Growth and the Formation of Spikes in the Surface of Supercooled Water

Abstract Observations made of ice crystals growing on the surface of supercooled water show that they take the form of a composite structure, called surface needles, each of which consists of dendrites growing into the liquid, and of ribs growing in the liquid surface. Each needle is a single crystal. The precise form of the needle is determined by the orientation of the initial nucleus. If its optic axis is near normal to the surface, growth occurs rapidly in two dimensions and covers a much larger proportion of the surface than is covered by the narrow surface needles, so that ice forming this way appears to have its optic axis vertical. Hollow ice spikes observed on pools are shown to have been formed by the freezing of water forced from beneath the surface at the intersection of two or three surface needles, the shape of the spike depending on their orientation.
Le contexte géologique des indices de talc de la région de Boumnyebel (Chaîne panafricaine d'Afrique Centrale, Cameroun)

De nouveaux levers cartographiques et une etude petrologique ont permis de redefinir la lithologie de la region de Boumnyebel et sa signification sur la chaine panafricaine d'Afrique centrale. Deux unites sont distinguees. Une premiere unite d? orthogneiss et amphibolites paleoproterozoiques affleure au sud et sud-ouest de la region d'etude. Elle est recouverte par une seconde unite panafricaine (nappe) constituee vers la base de micaschistes a grenat, amphibolites, metagabbros, hornblendites et pyroxenites, et vers le haut de micaschistes a grenat-disthene localement associes a des marbres et amphibolites ; des talcschistes s'intercalent en niveaux discontinus (=30 m) entre ces deux ensembles panafricains. La nature des facies de la partie inferieure de la nappe suggere l'existence d'une marge active a proximite d'une croute continentale (environnement d'arc ou d'arriere-arc), ceux de la partie superieure suggerant plutot un apport de sediments en provenance d'une croute continentale soumise a l'erosion. Le metamorphisme des formations panafricaines, de facies amphibolite, atteint la fusion (migmatites) au nord-est de la region etudiee. Le pic metamorphique (syn-D2) est estime a ~ 650- 670°C / ~ 9.5 kbar vers 620 Ma (datation Th-U-Pb sur monazite) et les isogrades sont en position normale. Ceci suggere que le pic thermique est posterieur a la mise en place de la nappe. Soulignons, enfin, que l'abondance des roches mafiques et ultramafiques de nature tholeitique dans la partie inferieure de la serie repose la question de l'existence d'une marge active au Nord du craton du Congo durant le Neoproterozoique.
Human immature testicular tissue organ culture: a step towards fertility preservation and restoration

Background Cryopreservation of immature testicular tissue (ITT) is currently the only option to preserve fertility of prepubertal patients. Autologous transplantation of ITT may not be safe or appropriate for all patients. Therefore, methods to mature ITT ex vivo are needed. Objectives Aim to investigate the feasibility of inducing in vitro spermatogenesis from ITT cryopreserved for pediatric patients prior to initiation of gonadotoxic therapy. Materials and methods Cryopreserved-thawed ITT from prepubertal and peripubertal patients were cultured for 7, 16, and 32 days in medium with no hormones or supplemented with 5 IU/L FSH, 1 IU/L hCG, or 5IU/L FSH+1 IU/L hCG. Samples were evaluated histologically to assess tissue integrity, and immunofluorescence staining was performed to identify VASA (DDX4)+ germ cells, UCHL1+ spermatogonia, SYCP3+ spermatocytes, CREM+ spermatids, SOX9+ Sertoli cells. Proliferation (KI67) and apoptosis (CASPASE3) of germ cells and Sertoli cells were also analyzed. Sertoli and Leydig cell maturation was evaluated by AR and INSL3 expression as well as expression of the blood testis barrier protein, CLAUDIN11, and testosterone secretion in the culture medium. Results Integrity of seminiferous tubules, VASA+ germ cells and SOX9+ Sertoli cells were maintained up to 32 days. The number of VASA+ germ cells was consistently higher in the peripubertal groups. UCHL1+ undifferentiated spermatogonia and SOX9+ Sertoli cell proliferation was confirmed in most samples. SYCP3+ primary spermatocytes began to appear by day 16 in both age groups. Sertoli cell maturation was demonstrated by AR expression but the expression of CLAUDIN11 was disorganized. Presence of mature and functional Leydig cells was verified by INSL3 expression and secretion of testosterone. Gonadotropin treatments did not consistently impact the number or proliferation of germ cells or somatic cells, but FSH was necessary to increase testosterone secretion over time in prepubertal samples. Conclusion ITT were maintained in organotypic culture for up to 32 days and spermatogonia differentiated to produce primary spermatocytes in both pre- and peripubertal age groups. However, complete spermatogenesis was not observed in either group.
How Fast Are Sea Levels Rising?

Sea levels are rising as a result of global warming, but assessing the rate of the rise is proving difficult. In his Perspective, Church highlights the report by Cabanes et al., who have reassessed observational data and find that it is closer to model estimates than previously found. However, observational data are still limited and models disagree in their regional projections. With present data and models, regional sea-level changes cannot be predicted with confidence.
Community Ecology of a Coral Cay: A Study of One-Tree Island, Great Barrier Reef, Australia

In this age of modern era, the use of internet must be maximized. Yeah, internet will help us very much not only for important thing but also for daily activities. Many people now, from any level can use internet. The sources of internet connection can also be enjoyed in many places. As one of the benefits is to get the on-line community ecology of coral cay a study of one tree island great barrier reef australia book, as the world window, as many people suggest.