Miracle-dz/UniFAR-FTUs huggingface dataset:
Contrasting Winter Versus Summer Microbial Communities and Metabolic Functions in a Permafrost Thaw Lake

Permafrost thawing results in the formation of thermokarst lakes, which are biogeochemical hotspots in northern landscapes and strong emitters of greenhouse gasses to the atmosphere. Most studies of thermokarst lakes have been in summer, despite the predominance of winter and ice-cover over much of the year, and the microbial ecology of these waters under ice remains poorly understood. Here we first compared the summer versus winter microbiomes of a subarctic thermokarst lake using DNA- and RNA-based 16S rRNA amplicon sequencing and qPCR. We then applied comparative metagenomics and used genomic bin reconstruction to compare the two seasons for changes in potential metabolic functions in the thermokarst lake microbiome. In summer, the microbial community was dominated by Actinobacteria and Betaproteobacteria, with phototrophic and aerobic pathways consistent with the utilization of labile and photodegraded substrates. The microbial community was strikingly different in winter, with dominance of methanogens, Planctomycetes, Chloroflexi and Deltaproteobacteria, along with various taxa of the Patescibacteria/Candidate Phyla Radiation (Parcubacteria, Microgenomates, Omnitrophica, Aminicenantes). The latter group was underestimated or absent in the amplicon survey, but accounted for about a third of the metagenomic reads. The winter lineages were associated with multiple reductive metabolic processes, fermentations and pathways for the mobilization and degradation of complex organic matter, along with a strong potential for syntrophy or cross-feeding. The results imply that the summer community represents a transient stage of the annual cycle, and that carbon dioxide and methane production continue through the prolonged season of ice cover via a taxonomically distinct winter community and diverse mechanisms of permafrost carbon transformation.
Kinematic calibration of parallel manipulators

Identification objective functions considering end effector pose errors and loop closure (branch end distance) errors for the calibration of parallel manipulators are discussed. Based on the elimination of the need for fixturing devices, loop closure error based objectives are demonstrated preferred. Kinematic calibration models for the RSI 6 degree of freedom hand controller including device geometric parameters are introduced. Calibrations considering more complete models are demonstrated to yield improved calibrations in comparison to models considering only original length, angle, and potentiometer parameters. To achieve higher precision, it is concluded that noise-free joint displacement sensing, and accurate passive spherical branch end joints are required.
Internet-delivered cognitive behavioral therapy for panic disorder with or without agoraphobia: a systematic review and meta-analysis

ABSTRACT The current systematic review and meta-analysis examined the efficacy and effectiveness of internet-delivered cognitive behavioral therapy (iCBT) on panic disorder and agoraphobia symptom severity. Twenty-seven studies were identified. Results from nine randomised controlled trials (RCTs) showed that iCBT outperformed waiting list and information controls for panic (g = 1.22) and agoraphobia (g = .91) symptoms, but the quality of RCTs varied and heterogeneity was high. Results from three RCTs suggested iCBT may have similar outcomes to face-to-face CBT in reducing panic and agoraphobia symptoms. Within-group effect sizes between baseline and post-treatment were large for panic (n = 29, g = 1.16) and medium for agoraphobia symptom severity (n = 18, g = .73). Subgroup analyses of within-group pre/post treatment effect sizes showed larger within-group effect sizes for efficacy studies (n = 15) compared to effectiveness studies (n = 14) for panic severity (g = 1.38 vs. g = .98) but not agoraphobia severity. There was no impact of program length, inclusion or arousal reduction techniques, or degree of clinician support. Within-group effects of iCBT suggest the reduction in panic and agoraphobia symptom severity is maintained at 3–6 month follow-up (n = 12).
Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells

Background HIV-1-infected cells in peripheral blood can be grouped into different transcriptional subclasses. Quantifying the turnover of these cellular subclasses can provide important insights into the viral life cycle and the generation and maintenance of latently infected cells. Results We used previously published data from five patients chronically infected with HIV-1 that initiated combination antiretroviral therapy (cART). Patient-matched PCR for unspliced and multiply spliced viral RNAs combined with limiting dilution analysis provided measurements of transcriptional profiles at the single cell level. Furthermore, measurement of intracellular transcripts and extracellular virion-enclosed HIV-1 RNA allowed us to distinguish productive from non-productive cells. We developed a mathematical model describing the dynamics of plasma virus and the transcriptional subclasses of HIV-1-infected cells. Fitting the model to the data allowed us to better understand the phenotype of different transcriptional subclasses and their contribution to the overall turnover of HIV-1 before and during cART. The average number of virus-producing cells in peripheral blood is small during chronic infection (25.7 cells ml−1). We find that 14.0%, 0.3% and 21.2% of infected cells become defectively, latently and persistently infected cells, respectively. Assuming that the infection is homogenous throughout the body, we estimate an average in vivo viral burst size of 2.1 × 104 virions per cell. Conclusions Our study provides novel quantitative insights into the turnover and development of different subclasses of HIV-1-infected cells. The model predicts that the pool of latently infected cells becomes rapidly established during the first months of acute infection and continues to increase slowly during the first years of chronic infection. Having a detailed understanding of this process will be useful for the evaluation of viral eradication strategies that aim to deplete the latent reservoir of HIV-1.
An optimization method for load management scheduling

Many utilities have load management programs whereby they directly control residential appliances in their service area. An algorithm for scheduling the load control using dynamic programming is presented. This method is based on an analytic dynamic model of the load under control. The method can be used for different utility objectives, including minimizing production cost and minimizing peak load over a period of time. >
Disease modeling of core pre-mRNA splicing factor haploinsufficiency

Abstract The craniofacial disorder mandibulofacial dysostosis Guion-Almeida type is caused by haploinsufficiency of the U5 snRNP gene EFTUD2/SNU114. However, it is unclear how reduced expression of this core pre-mRNA splicing factor leads to craniofacial defects. Here we use a CRISPR-Cas9 nickase strategy to generate a human EFTUD2-knockdown cell line and show that reduced expression of EFTUD2 leads to diminished proliferative ability of these cells, increased sensitivity to endoplasmic reticulum (ER) stress and the mis-expression of several genes involved in the ER stress response. RNA-Seq analysis of the EFTUD2-knockdown cell line revealed transcriptome-wide changes in gene expression, with an enrichment for genes associated with processes involved in craniofacial development. Additionally, our RNA-Seq data identified widespread mis-splicing in EFTUD2-knockdown cells. Analysis of the functional and physical characteristics of mis-spliced pre-mRNAs highlighted conserved properties, including length and splice site strengths, of retained introns and skipped exons in our disease model. We also identified enriched processes associated with the affected genes, including cell death, cell and organ morphology and embryonic development. Together, these data support a model in which EFTUD2 haploinsufficiency leads to the mis-splicing of a distinct subset of pre-mRNAs with a widespread effect on gene expression, including altering the expression of ER stress response genes and genes involved in the development of the craniofacial region. The increased burden of unfolded proteins in the ER resulting from mis-splicing would exceed the capacity of the defective ER stress response, inducing apoptosis in cranial neural crest cells that would result in craniofacial abnormalities during development.
Application of AR based model in proactive management of VBR traffic

Variable bit rate (VBR) video is expected to be dominant in ATM based B-ISDN networks. The characteristics of VBR traffic such as high peak-to-mean bit rate ratio and stochastic variations of bit rate with respect to time, however, make bandwidth allocation quite difficult. Choosing peak rate as a criteria would mean under-utilization of the available network bandwidth, whereas, allocating bandwidth based on mean rate would lead to congestion in the network. The effect of large delay-bandwidth product, in ATM networks, also adds to the complexity and renders conventional reactive based congestion control schemes as highly inefficient. Bandwidth allocation based on the mean rate, aided with a proactive congestion control scheme that could predict the onset of congestion well in advance, is, therefore, the desired solution for managing VBR traffic in ATM networks. One such estimation and prediction based approach to traffic control and congestion avoidance is proposed herein. The traffic from the VBR source(s) is modelled as an AR modulated process. The call arrival is assumed to be a birth-death process. Using these models the current traffic state is estimated, the future traffic states are predicted and the occurrence of congestion in the network is forecasted. Some simulation results are presented to verify the validity of the model and illustrate the effectiveness of the technique.
Effect of Camellia sinensis, Hypericum perforatum and Urtica dioica on kidney and liver injury induced by carbon tetrachloride in rats.

This study is aimed to investigate the effects of Camellia sinensis (CS), Hypericum perforatum (HP) and Urtica dioica (UD) in kidney and liver injury induced by carbon tetrachloride (CCl4) in rats. Highly toxic CCl4 which is used as a solvent in industry comprises experimental toxicity in rats and is widely used in hepatotoxicity and other tissue injury models. The purpose of this investigation is to monitor blood and various tissues by biochemical and histopathological analysis for preventive effects of CS, HP and UD on oxidative stress induced by administration of CCl4 and to enlighten the probable mechanism. Fifty eight rats were divided into five groups; sham group (Group 1, untreated animals), control CCl4 treated group (Group 2), HP extract-treated group (Group 3), UD extract-treated group (Group 4), CS extract-treated group (Group 5). All rats were anaesthetized at the end of the experiment and the blood was collected from each rat. Afterwards, tissue specimens were obtained. The tissue specimens were immersed in 10% formaldehyde for 24 hours. After routine tissue processing, the liver, kidney and stomach were sectioned in 5µm thickness, stained in hematoxylin and eosin. The histological study was performed by using light microscope. The serum marker enzymes were found to be significantly increased in CCl4-induced liver and kidney damage when compared with the sham group (p<0.05). However, treatment with CS, HP, and UD extracts resulted in decreased activity of serum enzymes. Malondialdehyde (MDA) levels were decreased by 20.51±0.95, 27.98±1.58, and 32.39±3.1 nmol/g wet weight protein in kidney homogenates and 16.65±1.75, 17.22±0.71 and 18.92±71 nmol/g wet weight protein in liver homogenates in CS, HP and UD treated groups, respectively. Our results have shown that additive antioxidants like CS, HP and UD will aid in diminishing these deviations in cases of liver and kidney dysfunction.
Perforator Flap Reconstruction for the Distal Third of Lower Extremity Defects: Clinical Application and Guideline Recommendation

A distal third of lower extremity defect is challenging for plastic surgeons. The standard for treatment is microsurgery. Recently, perforator flap has been reported for small to medium defects. The objective was to analyze the outcomes of perforator flaps for distal third of lower extremity defects and to establish surgical guidelines. A retrospective review of patients with defects in distal third of lower extremities was conducted. Patients with multiple levels of lower extremity defects were excluded. A total of 8 patients with distal third of lower extremity defects were included. Seven patients were male. Overall mean age was 35.3 (18-60) years. Patients had 3 anterior, 3 lateral, and 2 medial defects. Lateral and anterior defects in 6 patients were closed using a peroneal-based propeller perforator flap with an angle of rotation of 90° to 160°. Medial defects in 2 patients were closed using a posterior tibial-based perforator advancement flap. Three patients (37.5%) developed venous congestion. No complications occurred for patients with medial defect closure using an advancement posterior tibial-based perforator flap. No total flap loss was observed. The perforator flap provides a similar texture to the skin at recipient area and a wide range of rotation. Perforator flaps should be the first choice for defects reconstruction in distal third lower extremities. Perforator flaps can be used for small to large defects, and can be moved by propeller or advancement depending on the perforator location. A guideline for perforator flaps reconstruction of the distal third of lower extremity defects was established.
Robot-Crawler: Statically Balanced Gaits

This paper presents a new statically balanced walking technique for a robot-crawler. The gait design and the control of the robot crawler aim to achieve stability while walking. This statically balanced gait has to be designed in a different fashion to a wheeled robot, as there are discrete changes in the support of the robot when its legs are lifted or placed on the ground. The stability of the robot depends on how the legs are positioned relative to the body and also on the sequence and timing with which the legs are lifted and placed. In order to reduce the risk of stability loss while walking, a measure for the robot stability (so-called stability margin) is typically used in the gait and motion planning. In this paper different biological behaviours of four-legged animals are studied and mapped on a quad-legrobot- crawler. Experiments were carried out on the forward walking gaits of lizards and horses. Based on these results, the stability margins of different gaits are discussed and compared.
Zika circulation, congenital syndrome, and current guidelines: making sense of it all for the traveller.

PURPOSE OF REVIEW Zika virus (ZIKV) swept through the Americas and led to recognition of its neurotropism. Zika circulation elsewhere in the world, nonvector transmission including maternal-fetal/sexual/transfusion routes, and additional reports on congenital Zika syndrome (CZS) and Guillain-Barré syndrome (GBS) have been published. RECENT FINDINGS In 2018-2019, ZIKV transmission occurred in Cuba, India, and is suspected to appear sporadically in other countries. Maternal-fetal ZIKV transmission appears to occur in about 26% of ZIKV-infected pregnant women. The US ZIKV Pregnancy and Infant Registry identified 6% of live births to have at least one ZIKV-associated birth defect; 9% had at least one neurodevelopmental abnormality; 1% had both. Infectious virus was rarely isolated from semen of ZIKV-infected male patients beyond day 38 after symptom onset. Brazilian blood donations had low ZIKV prevalence in 2015-2016; in the United States, screening donations was cost-effective only in the high mosquito season in Puerto Rico. SUMMARY ZIKV transmission continues; many countries with competent mosquitoes are at risk. Transmission can occur without detection where surveillance is poor and laboratory capacity limited. Travelers are important sentinels. Variations exist among ZIKV strains and Aedes mosquitoes that influence competence for transmission. Maternal-fetal transmission results in significant rates of abnormality. Identification of infectious virus in semen clarifies sexual transmission risk, with updated recommendations for preconception planning. ZIKV neurotropism requires further research and long-term follow-up.
Branching and oscillations in the epigenetic landscape of cell-fate determination

The well-known Waddington’s epigenetic landscape of cell-fate determination is not static but varies because of the dynamic gene regulation during development. However, existing mathematical models with few state variables and fixed parameters are inadequate in characterizing the temporal transformation of the landscape. Here we simulate a decision-switch model of gene regulation with more than two state variables and with time-varying repression among regulatory factors. We are able to demonstrate multi-lineage differentiation at different timescales that portrays the branching canals in Waddington’s illustration. We also present a repressilator-type system that activates suppressed genes via sustained oscillations in a flattened landscape, hence providing an alternative scheme for cellular reprogramming. The time-dependent parameters governed by gradient-based dynamics regulate cell differentiation, dedifferentiation and transdifferentiation. Our prediction integrates the theories of branching and structural oscillations in cell-fate determination, which reveals key temporal patterns of cell differentiation and associated diseases, such as cancer.
Ecient Analysis of Complex Changepoint Models

Time-series data often experiences abrupt changes in structure. If the time-series is to be modelled accurately then these changepoints must be taken into account. Many methods for detecting these changepoints, both heuristic and exact, have been developed and these are reviewed in this report. The report in particular looks at dynamic programming approaches and pruning methods which can be used to speed these methods up. The report concludes by discussing a few of the open questions which are still unresolved and which may form part of the authors prospective PhD next year.
Cytochrome C Oxidase Subunit-1(COX1) Gene in Tilapia (Oreochromis Niloticus): its Cloning and Characterization

The current study aimed to identify cytochrome c oxidase subunit 1 (ONCOX1) in Tilapia (Oreochromis niloticus) immunized by formalin-killed Flavobacterium columnarae. Suppressive subtractive hybridization (SSH) was utilized to construct a cDNA library and a semi-quantitative RT-PCR analysis used to examine Oreochromis niloticus cy- tochrome c oxidase subunit 1 (COX1) gene expression. The complete sequence of the COX1 has been deposited in the GenBank Database and assigned the accession number (GE647880). COX1 cDNA is composed of 1139 bps with a 1107 bps open reading frame, the predicted gene product is 369 amino acid with molecular weight of 40.16 kDa. The amino acid sequence revealed high identity with subunit 1 from Oreochromis mossambicus. Compared to s-actin, the semi-quantitative RT-PCR revealed that ONCOX1 expressed in tissues of stimulated fish as up-regulated gene suggesting that this member of COX genes is probably involved in the general immune response against the pathogenic bacteria.
Phylogeny of Calostoma, the gelatinous-stalked puffball, based on nuclear and mitochondrial ribosomal DNA sequences

Abstract Nucleotide sequence of the nuclear small and large subunit and the mitochondrial small and large ribosomal genes of Calostoma were used to investigate evolutionary relationships with other Basidiomycetes. In separate analyses with each gene, Calostoma was placed within the Boletales and outside the clades containing most gilled mushrooms, puffballs, stalked puffballs, earthstars, stinkhorns and nonboletalean Gasteromycetes. This contradicted previous taxonomic hypotheses. Calostoma was most closely related to Gyroporus, Pisolithus, and Scleroderma based on maximum parsimony and maximum likelihood analysis of the mitochondrial large ribosomal gene database, which contained several representatives of most genera of the Boletales. In three of the four gene trees Calostoma shows an unusually high number of inferred nucleotide substitutions relative to other Boletales; this corresponds to its extreme morphological divergence.
SAS Global Forum 2009 Posters

In 1801, the idea of using a circular image to portray frequency and amount was formalized by Playfair. These first "statistical charts" illustrated the number of inhabitants in major European cities by a set of hand-drawn circles, with the diameter of the circle indicating population thus enabling effective comparison by city. Today's bubble charts enable the same effective comparison of frequency of phenomena of interest but with two pronounced improvements. The first contemporary improvement is the addition of a location matrix-Cartesian coordinate system-to enable display of the bubble plots in relation to a second variable. More importantly, the second improvement is the ability to use computers to draw and replicate the bubble plots quickly and inexpensively. Utilizing SAS/GRAPH and PROC GPLOT to construct bubble plots saves both time and money. The resultant bubble plots effectively communicate contemporary research results with both simplicity and elegance, reaching a diverse research audience with information needed for vital decision-making processes.
A Modified Molecular Beacons–Based Multiplex Real-Time PCR Assay for Simultaneous Detection of Eight Foodborne Pathogens in a Single Reaction and Its Application

Abstract Foodborne disease outbreaks are often caused by one of the major pathogens. Early identification of the causal pathogen is crucial for disease control and prevention. We describe a real-time polymerase chain reaction (rtPCR) assay that can identify, in a single reaction, up to eight common foodborne bacterial pathogens, including Salmonella enterica subsp. enterica, Listeria monocytogenes, Escherichia coli O157, Vibrio parahaemolyticus, V. vulnificus, Campylobacter jejuni, Enterobacter sakazakii, and Shigella spp. This multiplex rtPCR assay takes advantage of modified molecular beacons and the multicolor combinational probe coding strategy to discriminate each pathogen and the homo-tag assisted non-dimer (HAND) system to prevent dimer formation. The detection limits of the assay ranged from 1.3×103 colony-forming units (CFU)/g stool (L. monocytogenes) to 1.6×104 CFU/g stool (Shigella spp.). The target genes were 100% specific as assessed on 986 reference strains covering 41 species since no cross.
Hybrid Integrated Lumped-Element Microwave Amplifiers

This paper describes the development of microwave lumped-element thin-film amplifiers.The basic design philosophy underlying lumped inductors and capacitors at microwave frequencies is reviewed, showing how Q's of 100 are achieved. A variety of tunable input, output, and interstage integrated lumped-element networks for transistor amplifiers were fabricated.The gain and efficiency of 2-GHz class-C operated transistors mounted in these circuits were comparable with the best performance achieved by the same transistors in less lossy coaxial circuits. The measured losses (1.2 dB) at 2 GHz were very close to those calculated using the design parameters. Single-stage amplifiers at 2 GHz achieved one watt of output power with 4 dB of gain. At somewhat lower power levels more than 6 dB of gain was achieved. The circuits allowed the operation of low-power level class-A amplifiers with over 13 dB of gain. Cascaded operation yielded more than 17 dB of gain with 0.8 watts of CW power. It is concluded that lumped elements can be fabricated by thin-fihn technology and will play an important role in microwave integrated circuits.