Miracle-dz/UniFAR-FTUs huggingface dataset:
A Subunit of Protein Kinase A Regulates Growth and Differentiation in the Fungus Mucor circinelloides

ABSTRACT The cyclic AMP (cAMP)-dependent protein kinase A (PKA) signaling pathway plays a role in regulating development, growth, and virulence in a number of fungi. To determine whether PKA plays a similar function in zygomycete fungi, a mutant of Mucor circinelloides was generated that lacks pkaR1, one of the regulatory subunits of PKA. The mutant showed a reduction in growth and alterations in germination rates, cell volume, germ tube length, and asexual sporulation. The lack of pkaR1 gene resulted in a highly decreased, but not null, cAMP binding activity and in a protein kinase activity that was still dependent on cAMP, although with a higher −/+ cAMP activity ratio, suggesting the existence of other cAMP binding activities. Consequently, three proteins analogous to pkaR1 were predicted from the recently sequenced genome of M. circinelloides and were named pkaR2, pkaR3, and pkaR4. Two of the proteins, pkaR2 and pkaR3, with cAMP binding activity were isolated from the wild-type strain and identified by mass spectrometry. The expression of all genes was detected at the mRNA level by semiquantitative reverse transcription-PCR, and they showed a differential expression at different developmental stages. This is the first time that a fungus is reported to have more than one gene encoding the regulatory subunit of PKA.
Identifying the Relevant Nodes Without Learning the Model

We propose a method to identify all the nodes that are relevant to compute all the conditional probability distributions for a given set of nodes. Our method is simple, effcient, consistent, and does not require learning a Bayesian network first. Therefore, our method can be applied to high-dimensional databases, e.g. gene expression databases.
Sequence and structural elements of methylation guide snoRNAs essential for site‐specific ribose methylation of pre‐rRNA

Site‐specific 2′‐O‐ribose methylation of eukaryotic rRNAs is guided by small nucleolar RNAs (snoRNAs). The methylation guide snoRNAs carry long perfect complementaries to rRNAs. These antisense elements are located either in the 5′ half or in the 3′ end region of the snoRNA, and are followed by the conserved D′ or D box motifs, respectively. An uninterrupted helix formed between the rRNA and the antisense element of the snoRNA, in conjunction with the adjacent D′ or D box, constitute the recognition signal for the putative methyltransferase. Here, we have identified an additional essential box element common to methylation guide snoRNAs, termed the C′ box. We show that the C′ box functions in concert with the D′ box and plays a crucial role in the methyltransfer reaction directed by the upstream antisense element and the D′ box. We also show that an internal fragment of U24 methylation guide snoRNA, encompassing the upstream antisense element and the D′ and C′ box motifs, can support the site‐specific methylation of rRNA. This strongly suggests that the C box of methylation guide snoRNAs plays an essential role in the methyltransfer reaction guided by the 3′‐terminal antisense element and the D box of the snoRNA.
A distributed multimedia communication system and its applications to E-learning

In this paper we report on a multimedia communication system including a VCoIP (Video Conferencing over IP) software with a distributed architecture and its applications for teaching scenarios. It is a simple, ready-to-use scheme for distributed presenting, recording and streaming multimedia content. We also introduce and investigate concepts and experiments to IPv6 user and session mobility, with the special focus on real-time video group communication. Index Terms — Video and multi media conferencing, Elearning, Mobile IPv6, Multicast Mobility
Combined Toxic Exposures and Human Health: Biomarkers of Exposure and Effect

Procedures for risk assessment of chemical mixtures, combined and cumulative exposures are under development, but the scientific database needs considerable expansion. In particular, there is a lack of knowledge on how to monitor effects of complex exposures, and there are few reviews on biomonitoring complex exposures. In this review we summarize articles in which biomonitoring techniques have been developed and used. Most examples describe techniques for biomonitoring effects which may detect early changes induced by many chemical stressors and which have the potential to accelerate data gathering. Some emphasis is put on endocrine disrupters acting via epigenetic mechanisms and on carcinogens. Solid evidence shows that these groups of chemicals can interact and even produce synergistic effects. They may act during sensitive time windows and biomonitoring their effects in epidemiological studies is a challenging task.
Coordination mechanism for postponement strategy with downward substitutable products

We consider a supply chain implements postponement strategy to provide two kinds of products with different performance and cost. The high-performance product has the full function of the lower one, therefore the supplier can satisfy the demand of low-performance product with the higher one as it runs out. Recalling the manufacturing process of postponement strategy that consists of two periods: the one at the beginning for the common components and the other for differentiation as more information is available, we optimize this two-period dynamic decision process for downward substitutable products. Regarding the optimal behavior of the centralized supply chain as a benchmark, a bi-direction compensation contract with substitution premium is proposed for the decentralized system composed of a manufacturer and a retailer with local benefits. Through partly imposing the overproduction risk of the common components to the retailer, committing to buy back the overstocks and put a premium on each unit of substitution, the contract motivates the retailer to order as much as the centralized system's optimal output. Furthermore, this contract is not only effective to achieve coordination, but flexible to split the profit of the system between the channel members in an arbitrary ratio, thus the supply chain is expected to get Pareto-improving.
Wetlands Mapping in North America by Decision Rule Classification Using MODIS and Ancillary Data

An up-to-date wetlands map based on remote sensing data at a continental scale is urgently needed for estimating global environmental change. In this study, a wetlands map of North America was developed using Moderate Resolution Imaging Spectroradiometer (MODIS) data obtained in 2008 and ancillary data. For this purpose, a decision rule classification method was developed relied upon the hierarchical characteristics of land types and prior knowledge about the geographical location of wetlands. Two hierarchical levels of land types were used to extract wetlands. At the first level, non-vegetation land types including water, snow, urban, and bare areas were separately extracted from vegetation land types using threshold methods. At the second level, wetlands were discriminated from non-wetland vegetation land types with the MODIS tasseled cap (brightness, greenness, and wetness) indices using the decision tree method. In addition, elevation data were used to build the elevation mask and a climate map was used to subdivide the study area into five sub-regions. In the quantitative accuracy assessment, user's and producer's accuracies of wetlands for the whole study area were calculated as 80.3% and 83.7%, respectively. In a comparison with two existing global land cover datasets, GLC2000 and IGBP DISCover, our results show significant improvement in extracting coastal and narrow types of wetlands. This study indicates that decision rule classification, integrated with multi-temporal MODIS data and ancillary data, is useful to develop an improved wetlands map at a continental scale.
A statewide screening of mental health symptoms among juvenile offenders in detention.

OBJECTIVE As awareness of the high prevalence of mental health problems among juvenile offenders has grown, researchers and practitioners have recognized the need for reliable and efficient methods of assessing such problems among large numbers of offenders to ensure that limited treatment resources are applied to those with the greatest need. METHOD Between May 2000 and October 2002, 18,607 admissions were administered the computerized version of the Massachusetts Youth Screening Instrument Version 2 (MAYSI-2) 24 to 48 hours after their arrival at detention centers throughout Pennsylvania. RESULTS Approximately 70% of the males and 81% of the females scored above the clinical cutoff on at least one of the following five MAYSI-2 scales: Alcohol/Drug Use, Angry-Irritable, Depressed-Anxious, Somatic Complaints, and/or Suicide Ideation. Girls were more likely than boys to exhibit internalizing as well as externalizing problems. Mental health problems were most prevalent among white youths and least prevalent among African American youths. When youths repeated the screen upon subsequent visits to detention, their scores generally remained stable. CONCLUSIONS The findings suggest that the MAYSI-2 is a promising triage tool for emergent risk. The use of such a screen may reduce bias in allocation of treatment resources and improves our understanding of the nature of mental health problems in delinquent populations.
Learning Multimodal Temporal Representation for Dubbing Detection in Broadcast Media

Person discovery in the absence of prior identity knowledge requires accurate association of visual and auditory cues. In broadcast data, multimodal analysis faces additional challenges due to narrated voices over muted scenes or dubbing in different languages. To address these challenges, we define and analyze the problem of dubbing detection in broadcast data, which has not been explored before. We propose a method to represent the temporal relationship between the auditory and visual streams. This method consists of canonical correlation analysis to learn a joint multimodal space, and long short term memory (LSTM) networks to model cross-modality temporal dependencies. Our contributions also include the introduction of a newly acquired dataset of face-speech segments from TV data, which we have made publicly available. The proposed method achieves promising performance on this real world dataset as compared to several baselines.
Ultra-thin decoupled plasma nitridation (DPN) oxynitride gate dielectric for 80-nm advanced technology

Balancing gate leakage reduction, device performance, and gate dielectric reliability is a major challenge for oxynitride used as a gate dielectric for advanced technology. As compared to RTONO oxynitride, pMOSFET threshold voltage shift and transconductance degradation have been problematic for devices using remote plasma nitridation (RPN) or decoupled plasma nitridation (DPN) process due to non-optimal nitrogen profile in the film. In this paper, we report that the nitrogen profile of DPN gate dielectric can be engineered primarily by tuning the plasma pressure after optimizing other DPN process parameters to solve these problems. An EOT of 15 /spl Aring/ (23-/spl Aring/ NMOS CETinv) DPN oxynitride is demonstrated to have an acceptable pMOS Vt, comparable transconductance, significantly (/spl sim/30/spl times/) longer pMOS time-to-breakdown reliability for packaged devices, and 5/spl times/ gate leakage reduction relative to a high quality RTONO used in industry. The high quality ultrathin DPN film is fabricated in a commercially available system, which is compatible with standard CMOS processing technology. These encouraging results make high-pressure DPN oxynitride an attractive gate dielectric candidate for 80-nm advanced technology and beyond.
Brain imaging from the nano- to the macro-scale

A single imaging technique can reveal only a small part of the brains' complex machinery. Here, we present a correlative framework to combine complementary imaging technique and obtain a more comprehensive view of the encephalon. The same neuron imaged in vivo with two-photon fluorescence microscopy could be retrieved ex-vivo and characterized in terms of its ultrastructural features by means of electron microscopy. On the other hand, we describe a method to integrate data from in vivo two-photon fluorescence imaging and ex vivo light sheet microscopy, based on the use of major blood vessels as reference chart. This correlative approach allows placing in a three-dimensional anatomic context the neurons whose dynamics have been observed with high detail in vivo.
Segmented switched reluctance motor with novel winding and excitation strategy

In switched reluctance machine (SRM), the power density is increased by using full pitched winding instead of concentrated winding. It is reported that segmented switched reluctance machine (SSRM) using full pitched winding can give 40 – 75 % higher torque than conventional SRM for the same frame size. This increase in torque is due to the increase in aligned inductance. However, full pitch winding results in high copper loss, and high active weight. Hence, in this paper, single tooth or concentric winding to replace the full pitch winding of SSRM is proposed. In order to obtain the same flux paths as with full pitch winding, all the three phases must be excited simultaneously. The torque is produced due to changes in mutual inductance. This method of winding results in reduction of copper, and therefore, weight. With such an arrangement, one phase only requires DC supply, while other two phases must be excited with AC.
Heterogeneous modulation of exciton emission in triangular WS2 monolayers by chemical treatment

Chemical treatments were recently shown to be very effective in enhancing the exciton emission of monolayer transition metal dichalcogenides (1L-TMDs) by suppressing the exciton quenching caused by structural defects. However, the effects of these chemical treatments varied greatly depending on the synthesis method and the type of 1L-TMD; therefore, the exact origin of the emission enhancement is still elusive. Here we report the spatially heterogeneous effects of bis(trifluoromethane)sulfonimide (TFSI) and benzyl viologen (BV) treatment on the optical properties of triangular 1L-WS2 grown by chemical vapor deposition (CVD). Nanoscale photoluminescence (PL) and Raman spectral maps showed that TFSI had a minimal effect on the inner region of the triangular WS2 grain, whereas the PL of the edge region was enhanced up to 25 times; further, BV reduced the PL, also more strikingly in the edge region. Systematic variation of the spectral weights among neutral excitons, trions, and bi-excitons indicated that p-doping and n-doping with TFSI and BV, respectively, occurred in both the inner and edge regions; however, the PL enhancement was attributed mainly to the reduction of structural defects caused by TFSI treatment. Our observation of the spatially heterogeneous effects of chemical treatment suggests that the inner and edge regions of CVD-grown 1L-WS2 are populated with different types of structural defects and helps in clarifying the mechanism by which chemical treatment enhances the optical properties of 1L-TMDs.
Electric fields in bone marrow substructures at power-line frequencies

Bone marrow is known to be responsible for leukemia. In order to study the hypothesis relating power-line frequencies electromagnetic fields and childhood leukemia from a subcellular perspective, two models of bone marrow substructures exposed to electric field are computed numerically. A set of cancellous bone data obtained from computed tomography scan is computed using both the finite element method (FEM) and scalar potential finite difference method. A maximum electric field enhancement of 50% is observed. Another model of bone marrow stroma cells is implemented only in FEM using thin film approximation. The transmembrane potential (TMP) change across the gap junctions is found to range from several to over 200 /spl mu/V. The two results suggest that imperceptible contact currents can produce biologically significant TMP change at least in a limited number of bone marrow stroma cells.
Clinical and esthetic outcomes of implants placed in postextraction sites.

PURPOSE The aim of this review was to evaluate the clinical outcomes for the different time points of implant placement following tooth extraction. MATERIALS AND METHODS A PubMed search and a hand search of selected journals were performed to identify clinical studies published in English that reported on outcomes of implants in postextraction sites. Only studies that included 10 or more patients were accepted. For implant success/survival outcomes, only studies with a mean follow-up period of at least 12 months from the time of implant placement were included. The following outcomes were identified: (1) change in peri-implant defect dimension, (2) implant survival and success, and (3) esthetic outcomes. RESULTS AND CONCLUSIONS Of 1,107 abstracts and 170 full-text articles considered, 91 studies met the inclusion criteria for this review. Bone augmentation procedures are effective in promoting bone fill and defect resolution at implants in postextraction sites, and are more successful with immediate (type 1) and early placement (type 2 and type 3) than with late placement (type 4). The majority of studies reported survival rates of over 95%. Similar survival rates were observed for immediate (type 1) and early (type 2) placement. Recession of the facial mucosal margin is common with immediate (type 1) placement. Risk indicators included a thin tissue biotype, a facial malposition of the implant, and a thin or damaged facial bone wall. Early implant placement (type 2 and type 3) is associated with a lower frequency of mucosal recession compared to immediate placement (type 1).
Antigenic S-type lipopolysaccharide of Brucella abortus 1119-3

Antigenic phenol-phase soluble lipopolysaccharide isolated from Brucella abortus 1119-3 by hot phenol-water extraction was shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, controlled hydrolysis, periodate oxidation, methylation, and 1H and 13C nuclear magnetic resonance studies to be an S-type lipopolysaccharide which could be cleaved to yield a lipid A and an O-chain polysaccharide identified as an unbranched linear homopolymer of 1,2-linked 4,6-dideoxy-4-formamido-alpha-D-mannopyranosyl residues. The serological reactivity of bovine antiserum to B. abortus 1119-3 with the lipopolysaccharides of Yersinia enterocolitica serotype O:9 and Vibrio cholerae species has now been related to the occurrence of 1,2-linked N-acylated 4-amino-4,6-dideoxy-alpha-D-mannopyranosyl units in the O-chain polysaccharides of their lipopolysaccharides.
Interaction between Dietary Methionine and Methyl Donor Intake on Rat Liver Betaine-homocysteine Methyltransferase Gene Expression and Organization of the Human Gene*

We previously showed that rat liver betaine-homocysteine methyltransferase (BHMT) mRNA content and activity increased 4-fold when rats were fed a methionine-deficient diet containing adequate choline, compared with rats fed the same diet with control levels of methionine (Park, E. I., Renduchintala, M. S., and Garrow, T. A. (1997) J. Nutr. Biochem.8, 541–545). A further 2-fold increase was observed in rats fed the methionine-deficient diet with supplemental betaine. The nutrition studies reported here were designed to determine whether other methyl donors would induce rat liver BHMT gene expression when added to a methionine-deficient diet and to define the relationship between the degree of methionine restriction and level of methyl donor intake on BHMT expression. Therefore, rats were fed amino acid-defined diets varying in methionine and methyl donor composition. The effect of diet on BHMT expression was evaluated using Northern, Western, and enzyme activity analyses. Similar to when betaine was added to a methionine-deficient diet, choline or sulfonium analogs of betaine induced BHMT expression. The diet-induced induction of hepatic BHMT activity was mediated by increases in the steady-state level of its mRNA and immunodetectable protein. Using methyl donor-free diets, we found that methionine restriction was required but alone not sufficient for the high induction of BHMT expression. Concomitant with methionine restriction, dietary methyl groups were required for high levels of BHMT induction, and a dose-dependent relationship was observed between methyl donor intake and BHMT induction. Furthermore, the severity of methionine restriction influenced the magnitude of BHMT induction. To study the molecular mechanisms that regulate the expression of BHMT, we have cloned the human BHMT gene. This gene spans about 20 kilobases of DNA and contains 8 exons and 7 introns. Using RNA isolated from human liver and hepatoma cells, a major transcriptional start site has been mapped using the 5′ rapid amplification of cDNA ends technique, and this start site is 26 nucleotides downstream from a putative TATA box.
Role of sympathetic nerves in the vascular effects of local temperature in human forearm skin.

The role of adrenergic nerve function in the cutaneous vascular response to changes in local skin temperature in the human forearm was examined using three protocols: 1) blocking release of norepinephrine presynaptically by local iontophoresis of bretylium (BT), 2) altering background adrenergic tone by changing whole body skin temperature, and 3) blocking cutaneous nerves by proximal infiltration of local anesthetic. Forearm skin blood flow was measured by laser-Doppler flowmetry (LDF) and cutaneous vascular conductance (CVC) was calculated as LDF/blood pressure. In protocol 1, local cooling (29 degrees C) elicited a rapid and sustained fall in CVC at control sites (-43 +/- 8%) in contrast to a biphasic response at BT-treated sites, consisting of an initial vasodilation followed by a vasoconstriction (percent change CVC = 28 +/- 13 and -34 +/- 18, respectively). Local warming (39 degrees C) increased CVC at control and at BT-treated sites by 331 +/- 46 and 139 +/- 31%, respectively. In protocol 2, at a neutral, cool, or warm whole body skin temperature, local cooling (29 degrees C) elicited similar reductions in CVC (-34 +/- 8, -29 +/- 5, and -30 +/- 4%, respectively), and local warming (38 degrees C) produced similar increases in CVC (89 +/- 15, 85 +/- 21, and 74 +/- 22%, respectively). (ABSTRACT TRUNCATED AT 250 WORDS)
Solving an Empirical Puzzle in the Capital Asset Pricing Model

A long standing puzzle in the Capital Asset Pricing Model (CAPM) has been the inability of empirical work to validate it. This paper presents a new approach to estimating the CAPM, taking into account the differences between observable and expected returns for risky assets and for the market portfolio of all traded assets, as well as inherent nonlinearities and the effects of excluded variables. Using this approach, we provide evidence that the relation between the observable returns on stock and market portfolios is nonlinear.
Sidelobe suppression for OFDM based cognitive radio systems

This paper investigates the sidelobe suppression techniques of Orthogonal Frequency Division Multiplexing (OFDM) based Cognitive Radio (CR) systems. We firstly argue that the existing sidelobe suppression algorithms cannot satisfy the special requirements of CR systems. Then we formulate the interference suppression problem of CR systems into two algorithms from capacity perspective, namely, average power allocation with cancellation subcarrier (CCs) scheme and adaptive subcarrier weighting scheme. We show that the capacity of the two schemes can well approximate the ideal waterfilling algorithm performance. We further show that under tough interference suppression requirement of licensed users (LU), the adaptive subcarrier weighting scheme is a better choice for CR systems.