Miracle-dz/UniFAR-FTUs huggingface dataset:
Into the Evening: Complex Interactions in the Arabidopsis circadian clock

In Arabidopsis thaliana, an assembly of proteins named the evening complex (EC) has been established as an essential component of the circadian clock with conserved functions in regulating plant growth and development. Recent studies identifying EC-regulated genes and EC-interacting proteins have expanded our understanding of EC function. In this review, we focus on new progress uncovering how the EC contributes to the circadian network through the integration of environmental inputs and the direct regulation of key clock genes. We also summarize new findings of how the EC directly regulates clock outputs, such as day-length dependent and thermoresponsive growth, and provide new perspectives on future experiments to address unsolved questions related to the EC.
A low jitter PLL using high PSRR low-dropout regulator

of the Thesis A Low Jitter PLL Using High PSRR Low-Dropout Regulator by Gyunam Jeon Master of Science in Electrical and Computer Engineering Northeastern University, June 2015 Dr. Yong-Bin Kim, Adviser In the recent years, the world has seen a huge boom in portable electronic products like cell phones, tablets, etc. Most of the products are powered by a battery that requires a power supply noise management circuitry to optimize the performance. As a result, lots of recent researches have been proposed across the world in battery’s power supply noise management field to improve power consumption and also to reduce the cost of integrated chips. Phase-Locked Loop (PLL) is a feedback system that forces a voltage controlled oscillator to replicate and track the frequency and phase at the input when in lock[1, 2]. It is a control system allowing one oscillator to track with another. The PLL is widely used and its usage is continuously increasing in modern integrated circuit design such as synthesizers and clock generators [3].
Short-Term Effects of Air Pollution on Heart Rate Variability in Senior Adults in Steubenville, Ohio

Objective: We examined the association between ambient air pollution levels and heart rate variability (HRV) in a panel study of 32 subjects. Methods: We used linear mixed models to analyze the effects of fine particles (PM2.5), sulfate (SO42−), elemental carbon (EC), and gases on log-transformed standard deviation of normal RR intervals (SDNN), mean square of differences between adjacent RR intervals (r-MSSD), and high- and low-frequency power (HF, LF). Results: An interquartile range (IQR) increase of 5.1 &mgr;g/m3 in SO42− on the previous day was associated with a decrease of −3.3% SDNN (95% confidence = −6.0% to −0.5%), −5.6% r-MSSD (−10.7% to −0.2%), and −10.3% HF (−19.5% to −0.1%). Associations with total PM2.5 were similar. HRV was not associated with EC, NO2, SO2, or O3. Conclusion: In addition to traffic-related particles, elevated levels of sulfate particles may also adversely affect autonomic function.
Transplantation of Human Adipose Tissue-Derived Stem Cells Delays Clinical Onset and Prolongs Life Span in ALS Mouse Model

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that selectively affects motor neurons in the cortex, brain stem, and spinal cord. The precise pathogenic mechanism remains unknown, and there is currently no effective therapy. We evaluated the therapeutic effects of human adipose tissue-derived stem cells (ASCs) in an animal model of ALS. Human abdominal subcutaneous fat tissues were obtained by simple liposuction from donors, and ASCs were isolated from the fat stromal vascular fraction. ASCs were found to differentiate into adipocytes, chondrocytes, osteocytes, and neurons. SOD1G93A ALS mice were divided into three groups: sham, intravenous (IV), and intracerebroventricular (ICV) groups. Human ASCs were transplanted in the ALS mice at 70 postnatal days before the appearance of clinical symptoms. Behavior of transplanted animals was assessed by rotarod test, paw grip endurance (PaGE), and reflex index. Mice in every group were sacrificed after 4 weeks posttransplantation. Transplanted ASCs were identified in the lumbar spinal cords with an antihuman mitochondria antibody and cell type-specific markers for neurons or astrocytes. Delayed onset of clinical symptoms (26 days) and extended survival of animals (24 days) were observed in ALS mice transplanted with ASCs via ICV route. ASCs were found to secrete high levels of neurotrophic factors such as NGF, BDNF, IGF-1, and VEGF. Reduction of apoptotic cell death by these factors was confirmed in cultured CNS cells and in the ALS spinal cord. These results indicate that transplantation of ASCs in ALS mice provides neuroprotective effects by production of cytokines/growth factors, delays disease progression, and prolongs the life span of ALS mice.
Effect of Dietary Gelatinized Starch Level and Rearing Temperature on Fatty Acid Profile and DNA:RNA Ratio of Labeo rohita (Hamilton) Fingerlings

A 60-day feeding trial was conducted to delineate the effect of three dietary levels of gelatinized starch on fatty acid profiles and RNA and DNA contents of fingerlings of the Indian major carp, Labeo rohita, reared at ambient water temperature (26±0.8°C) or 32°C. Two hundred and sixteen fingerlings (6.5±0.3 g) were randomly distributed into six treatments in triplicate. Three semi-purified isonitrogenous diets were prepared with 40%, 50%, or 58% gelatinized starch. Liver and muscle RNA and RNA:DNA ratio were significantly (p 0.05). Total saturated fatty acids (SAFA) in muscle was highest in fish fed the 50% diet; SAFA in fish fed the 58% diet were higher than in those fed the 40% diet but lower than in those fed the 50% diet. Polyunsaturated fatty acids (PUFA) were highest in fish fed the 40% diet. Total n-3 and n-6 fatty acids generally decreased as the level of starch increased; likewise, higher levels of gelatinized starch led to a reduced n-3:n-6 ratio. Rearing temperature had no significant effect on fatty acid composition of the muscle. RNA content and RNA:DNA ratio in the liver and muscle decreased gradually as the starch level
Complementation of Brucella abortus RB51 with a Functional wboA Gene Results in O-Antigen Synthesis and Enhanced Vaccine Efficacy but No Change in Rough Phenotype and Attenuation

ABSTRACT Brucella abortus RB51 is a stable rough, attenuated mutant vaccine strain derived from the virulent strain 2308. Recently, we demonstrated that the wboA gene in RB51 is disrupted by an IS711 element (R. Vemulapalli, J. R. McQuiston, G. G. Schurig, N. Srirauganathan, S. M. Halling, and S. M. Boyle, Clin. Diagn. Lab. Immunol. 6:760–764, 1999). Disruption of the wboA gene in smooth, virulent B. abortus, Brucella melitensis, and Brucella suis results in rough, attenuated mutants which fail to produce the O polysaccharide (O antigen). In this study, we explored whether the wboA gene disruption is responsible for the rough phenotype of RB51. We complemented RB51 with a functionalwboA gene, and the resulting strain was designated RB51WboA. Colony and Western blot analyses indicated that RB51WboA expressed the O antigen; immunoelectron microscopy revealed that the O antigen was present in the cytoplasm. Crystal violet staining, acryflavin agglutination, and polymyxin B sensitivity studies indicated that RB51WboA had rough phenotypic characteristics similar to those of RB51. Bacterial clearance studies of BALB/c mice indicated no increase in the survival ability of RB51WboA in vivo compared to that of RB51. Vaccination of mice with live RB51WboA induced antibodies to the O antigen which were predominantly of the immunoglobulin G2a (IgG2a) and IgG3 isotypes. After in vitro stimulation of splenocytes with killed bacterial cells, quantitation of gamma interferon in the culture supernatants indicated that RB51WboA immunization induced higher levels of gamma interferon than immunization with RB51. Mice vaccinated with RB51WboA were better protected against a challenge infection with the virulent strain 2308 than those vaccinated with RB51. These studies indicate that in addition to the disruption of the wboAgene there is at least one other mutation in RB51 responsible for its rough phenotype. These studies also suggest that the expressed O antigen in RB51WboA is responsible either directly or indirectly for the observed enhancement in the T-cell response.
Activation of plasma membrane H(+)-ATPase and expression of PMA1 and PMA2 genes in Saccharomyces cerevisiae cells grown at supraoptimal temperatures

During exponential growth at temperatures of 30 to 39 degrees C, the specific activity of H(+)-ATPase in the plasma membrane of Saccharomyces cerevisiae (assayed at the standard temperature 30 degrees C) increased with increases in growth temperature. In addition, the optimal temperature for in vitro activity of this ATPase was 42 degrees C. Therefore, the maximum values of ATPase activity were expected to occur in cells that grew within the supraoptimal range of temperatures. Activation induced by supraoptimal temperatures was not the result of increased synthesis of this membrane enzyme. When the growth temperature increased from 30 to 40 degrees C, expression of the essential PMA1 gene, monitored either by the level of PMA1 mRNA or the beta-galactosidase activity of the lacZ-PMA1 fusion, was reduced. Consistently, quantitative immunoassays showed that the ATPase content in the plasma membrane decreased. Like ATPase activity, the efficiency of the PMA2 promoter increased with increases in growth temperature in cells that had been grown at 30 to 39 degrees C, but its level of expression was several hundred-fold lower than that of PMA1. These results suggest that the major PMA1 ATPase is activated at supraoptimal temperatures.
Research progress of relations between exercise training and obese chronic inflammatory

Obesity can be considered as a chronic, systemic low-grade inflammation state induced by different inflammatory cytokines. The chronic inflammation in obesity may be a result of hypoxia in adipose tissue, macrophage infiltration to vascular wall and endocytoplasmic reticulum stress. Studies have shown that long-time regular exercise training can lower the levels of inflammatory markers and reduce the inflammation in obesity. Exercise training may reduce chronic inflammation by promoting the release of muscle-derived IL-6, increasing the total adipose tissue oxygenation, inhibiting the macrophage infiltration, reducing the number of pro-inflammatory monocots, down regulating the Toll-like receptor expression, increased the number of regulatory T cells. It will provide new ideas for the clinical treatment of chronic inflammation through further investigating the molecular mechanisms by which exercise training reduces chronic, systemic inflammation in obese individuals.
RhoA Interacts with the Fusion Glycoprotein of Respiratory Syncytial Virus and Facilitates Virus-Induced Syncytium Formation

ABSTRACT The fusion glycoprotein (F) of respiratory syncytial virus (RSV), which mediates membrane fusion and virus entry, was shown to bind RhoA, a small GTPase, in yeast two-hybrid interaction studies. The interaction was confirmed in vivo by mammalian two-hybrid assay and in RSV-infected HEp-2 cells by coimmunoprecipitation. Furthermore, the interaction of F with RhoA was confirmed in vitro by enzyme-linked immunosorbent assay and biomolecular interaction analysis. Yeast two-hybrid interaction studies with various deletion mutants of F and with RhoA indicate that the key binding domains of these proteins are contained within, or overlap, amino acids 146 to 155 and 67 to 110, respectively. The biological significance of this interaction was studied in RSV-infected HEp-2 cells that were stably transfected to overexpress RhoA. There was a positive correlation between RhoA expression and RSV syncytium formation, indicating that RhoA can facilitate RSV-induced syncytium formation.
Usefulness of Serum Prolactin in Differentiating Epileptic and Pseudoseizures in Children

Transient hyperprolectinemia has been reported to follow unprovoked seizures. This study was conducted in 90 children aged 1-18 years of age. The study comprised of four groups: Group-1 consisted of children with epilepsy which was further subdivided into GTCS, CPS and SPS. Group-2 comprised of children having febrile convulsions. Group-3 comprised of children suffering from non-epileptic paroxysmal events like breath holding spell, syncope and pseudoseizures or conversion reaction. Group-4 consisted of children who served as controls. Blood sample was collected within two hours of the event in all the groups. The exact interval between the event and the collection of blood sample was noted. Serum prolactin level was estimated by ELISA technique. In the present study, significant elevation of serum prolactin level was observed only in the Group-1 (28.77+15.49ng/ml) as compared to controls (9.53+2.45ng/ml) and the highest levels were observed in children with GTCS. Maximum elevation of prolactin was seen within 15 to 30 minutes post ictally. As the prolactin levels become normal after two hours of post ictal period, the test looses its significance.
Designing new languages or new language manipulation systems using ML

The ML language and the denotational theory of programming languages fit together to yield a powerful tool in (new) language design. To effectively support this claim, we give a running definition of a simple Pascal-like programming language with a new and non-standard programming construct. All the provided exemples have been tested on a Unix-4.2BSD implementation of ML.
Trophic Factor Modulation of c-Jun Expression in Supraspinal Neurons after Chronic Spinal Cord Injury

Cervical, but not thoracic spinal cord injury upregulates, in certain brainstem neurons, the expression of c-Jun, an inducible transcription factor that may be involved in the regenerative program/cell body response to injury. This study was designed to evaluate changes in c-Jun expression over a long period after spinal cord injury and to determine if such expression could be influenced by trophic or growth factors. Adult rats received a cervical (C3) hemisection lesion. Four or eight weeks later the lesion site was exposed, scar tissue in the cavity was removed and gel foam saturated with ciliary neurotrophic factor (CNTF), basic fibroblast growth factor (FGF2), or phosphate-buffered saline (PBS) as a control was placed into the cavity. Animals were sacrificed 7 days after treatment. In response to axotomy, c-Jun expression remained elevated in the red nucleus (RN) and vestibular complex (VST) at 4 weeks after injury, with no changes observed following scar tissue removal and PBS treatment. In contrast, treatment with CNTF further increased expression by RN neurons, but not VST neurons. Treatment with FGF2 had no significant effect on c-Jun expression at 4 weeks after injury. After 8 weeks, c-Jun expression approached baseline levels; however, removal of scar tissue, with subsequent secondary injury, caused an upregulation of c-Jun expression in both RN and VST neurons, which could be enhanced by CNTF, but not FGF2, treatment. At long postinjury intervals, interventive therapy known to promote axonal regeneration from chronically injured neurons leads to a reinduction of c-Jun expression. This reinduction may be related to the initiation of the regenerative effort of these neurons, although the lack of c-Jun upregulation by certain types of neurons does not appear to prevent a regenerative response by these cells.
Extracting the Geometry of Buildings from Satellite Images Using Fuzzy Multiple Layer

This paper presents Computer Aided Architectural Design (CAAD) system utilizing the technologies of artificial intelligence (AI) and image processing. The goal is to create a CAAD system that detects buildings from satellite images and produces computer city models allowing the system’s users to manipulate the models utilizing machine learning technology. The flexibility and usability of the system was evaluated with case studies. Soft computing technologies including neural networks and fuzzy systems are mainly applied and tested as the system’s methodology.
Drug-induced causes of secondary hypertension.

Resistant hypertension is a blood pressure that remains above the treatment goal despite use of optimal doses of three antihypertensive drugs of different classes including a diuretic (1). Patients with resistant hypertension should be screened for causes of secondary hypertension (2). Common causes of secondary hypertension include renal parenchymal disease (1), renovascular disease (3), dug-induced causes (4), pregnancy (5), primary aldosteronism (6), and obstructive sleep apnea (7). Uncommon causes of secondary hypertension include acromegaly, hyperthyroidism, hypothyroidism, hyperparathyroidism, Cushing syndrome, apparent mineralocorticoid excess, pheochromocytoma/paraganglioma, carcinoid syndrome, congenital adrenal hyperplasia, coarctation of the aorta, and neurological causes (2). This article will discuss some of the drug-induced causes of secondary hypertension.
Growth and elongation within and along the axon

Mechanical tension is a particularly effective stimulus for axonal elongation, but little is known about how it leads to the formation of new axon. To better understand this process, we examined the movement of axonal branch points, beads bound to the axon, and docked mitochondria while monitoring axonal width. We found these markers moved in a pattern that suggests elongation occurs by viscoelastic stretching and volume addition along the axon. To test the coupling between “lengthening” and “growth,” we measured axonal width while forcing axons to grow and then pause by controlling the tension applied to the growth cone or to the cell body. We found axons thinned during high rates of elongation and thickened when the growth cones were stationary. These findings suggest that forces cause lengthening because they stretch the axon and that growth occurs, in a loosely coupled step, by volume addition along the axon. © 2009 Wiley Periodicals, Inc. Develop Neurobiol, 2010
Molecular mechanism of gentamicin resistance in Bartonella henselae.

mm) were measured every 2 weeks. The confluent growth outside the zone of inhibition was harvested with an inoculation loop and subcultured every 2 weeks until the strain became completely resistant. The B. henselae mutant strain obtained was screened for the presence of mutations in the 16S rDNA gene by PCR amplification and DNA sequencing using specific oligonucleotidic primers targeting the 16S rDNA gene. Primers used were Bh16SF1 (TTCAATATGAGAGTTTGA), Bh16SR1 (ACGGCTAACATTCATCGT) and Bh16SF2 (GAATTCCGAGTGTAGAGG), Bh16SR2 (AGAAAGGAGGTGATCCAG). The obtained nucleotide sequences of candidate genes were compared using the CLUSTAL W program (http://www.ebi.ac.uk/Tools/clustalw2/index.htm) to look at possible mutations known to be associated with antibiotic resistance.
A Bayesian approach for spatio-spectral filter optimization in BCI

In this paper, we propose a novel Bayesian frame-work for discriminative feature extraction for motor imagery classification in an EEG-based BCI, in which the class-discriminative frequency bands and the corresponding spatial filters are optimized by means of the probabilistic and information-theoretic approaches. In our framework, the problem of simultaneous spatio-spectral filter optimization is formulated as the estimation of an unknown posterior pdf that represents the probability that a single-trial EEG of predefined mental tasks can be discriminated in a state. We demonstrate the feasibility and effectiveness of the proposed method by analyzing the results and its success on two public databases.
Regulation of sterile inflammation in the natural resolution of venous thrombosis

http://dx.doi. org/10.1160/TH15-09-0750 Thromb Haemost 2015; 114: 875 Venous thrombi resolve naturally through a process of tissue organisation similar to that seen during wound healing, and it is increasingly becoming clear that the innate ‘sterile’ inflammatory system is intimately linked to this intravascular ‘healing’ process (1). The initial recruitment of neutrophils followed by their demise and accumulation of macrophages, is a consistent inflammatory signature of venous thrombus formation and subsequent resolution. These cells express a number of pattern recognition receptors (PRRs) that are activated by damage associated molecular patterns (DAMPs) from non-infectious cellular ‘debris’, causing the release of mediators that promote inflammation (2). DAMPs, present within thrombus, include DNA released from neutrophils (that also act as extracellular traps during thrombus formation) and factors such as uric acid and high mobility group box 1 (HMGB1), described in the manuscript by Dewyer et al in this issue (3). DNA and histones can alter the fibrin architecture in plasma clots by inhibiting plasminogen activation or protecting thrombin from inactivation, respectively, whereby neutrophil extracellular traps lead to decreased susceptibility of plasma clots to lytic resolution (4). In addition to these intracellular DAMPs, extracellular matrix degradation may also release fragments (e. g. biglycans and hyaluronans) that act as danger signals. It is likely, however, that release of haem from red cells, that form the largest cellular component of a venous thrombus, also significantly contributes to this pro-inflammatory signaling environment (5). Toll-like receptors are only one class of PPRs that sense these danger signals involved in sterile inflammation, and as the manuscript by Dewyer et al (3) concludes, a member of this family of receptors (TLR9), expressed on macrophages, appears to be important for normal thrombus resolution. Understanding the interaction between PPRs and their ligands, and how these affect inflammatory cell activities in the context of thrombus resolution, may lead to the discovery of therapeutic targets that reduce the incidence of the post-thrombotic syndrome. The precise mechanisms by which inflammatory cells remove the thrombus remain, however, to be defined.
Using microwave radar for soil moisture inversion under soybean canopies

The successful radar mapping of soil moisture under vegetation canopies would be a boon to agriculture, global climate change studies, water resource management and other areas. Toward this end, a series of polarimetric radar measurements of soybeans over the entire growing season of 1996 were made at L and C-band at the Long Term Ecological Research site at the Kellogg Biological Station, Hickory Corners, MI. The radar data obtained has been successfully modeled with a simplified radiative transfer expression, including the dependence of the VV,HH, and cross-polarized backscattering coefficients on the angle of incidence, vegetation water mass, vegetation height, and volumetric soil moisture. In addition, a simple inversion model based on the forward model has been obtained which yields vegetation water mass and volumetric soil moisture for select polarization and frequency combinations.