Miracle-dz/UniFAR-FTUs huggingface dataset:
Discrimination of Multiple Dehalococcoides Strains in a Trichloroethene Enrichment by Quantification of Their Reductive Dehalogenase Genes

ABSTRACT While many anaerobic microbial communities are capable of reductively dechlorinating tetrachloroethene (PCE) and trichloroethene (TCE) to dichloroethene (DCE), vinyl chloride (VC), and finally ethene, the accumulation of the highly toxic intermediates, cis-DCE (cDCE) and VC, presents a challenge for bioremediation processes. Members of the genus Dehalococcoides are apparently solely responsible for dechlorination beyond DCE, but isolates of Dehalococcoides each metabolize only a subset of PCE dechlorination intermediates and the interactions among distinct Dehalococcoides strains that result in complete dechlorination are not well understood. Here we apply quantitative PCR to 16S rRNA and reductase gene sequences to discriminate and track Dehalococcoides strains in a TCE enrichment derived from soil taken from the Alameda Naval Air Station (ANAS) using a four-gene plasmid standard. This standard increased experimental accuracy such that 16S rRNA and summed reductase gene copy numbers matched to within 10%. The ANAS culture was found to contain only a single Dehalococcoides 16S rRNA gene sequence, matching that of D. ethenogenes 195, but both the vcrA and tceA reductive dehalogenase genes. Quantities of these two genes in the enrichment summed to the quantity of the Dehalococcoides 16S rRNA gene. Further, between ANAS subcultures enriched on TCE, cDCE, or VC, the relative copy number of the two dehalogenases shifted 14-fold, indicating that the genes are present in two different Dehalococcoides strains. Comparison of cell yields in VC-, cDCE-, and TCE-enriched subcultures suggests that the tceA-containing strain is responsible for nearly all of the TCE and cDCE metabolism in ANAS, whereas the vcrA-containing strain is responsible for all of the VC metabolism.
Quantification of organic carbon from biomass versus non-biomass burning emissions to fine aerosol

In the present study, size-segregated aerosol samples (in five size ranges) were collected from Patiala (30.33°N, 76.40°E; 250m amsl), located in the northwestern Indo-Gangetic Plain (IGP) during October 2012 to September 2013 to quantify the contribution of biomass burning (BB) to ambient organic carbon (OC) in fine aerosol. All of these samples were analyzed for major inorganic ions, whereas, particulate matter smaller than 1 μm aerodynamic diameter (PM1) were also analyzed for carbonaceous aerosol (OC, elemental carbon (EC), and water-soluble organic carbon (WSOC)). The contribution of BB
Frequency and clinical features of Lewy body dementia in Italian memory clinics.

BACKGROUND The latest developments in Lewy Body Dementia (DLB) raise some controversies on clinical features, neuroimaging and therapy. The aim of our study is to determine clinical, neuropsychological, neuroimaging and EEG profile of DLB through retrospective and prospective data of 102 patients. METHODS data were collected with an analytical form that was developed by an expertise of neurologists. RESULTS DLB represented 4.8% of the dementia population, with no sex difference. Family history of dementia was common (24.5%), while familiarity for parkinsonism was rare (4.9%). Cognitive disturbances were the predominant clinical presentation at onset (49%), followed by behavioral symptoms (29.4%) and parkinsonism (21.6%). Clinical features at consultation were: memory disturbances (almost all cases), symmetrical (68.6%) or asymmetrical (18.6%) parkinsonism, cognitive fluctuations (49%), visuospatial deficits (53.9%), and visual hallucinations (44.1%). Autonomic signs were present in a third of the cases, while sleep disorders were present in 44.1%. Some clinical response to antiparkinsonian drugs was evident in half of the cases. MRI, SPET, EEG and Neuropsychiatric Inventory data were available in a subgroup of patients. CONCLUSIONS Most of our data were in accordance with the previous literature. However, some data underline the relationship between DLB, Alzheimer's and Parkinson's disease.
HCFI: Hardware-enforced Control-Flow Integrity

Control-flow hijacking is the principal method for code-reuse techniques like Return-oriented Programming (ROP) and Jump-oriented Programming (JOP). For defending against such attacks, the community has proposed Control-flow Integrity (CFI), a technique capable of preventing exploitation by verifying that every (indirect) control-flow transfer points to a legitimate address. Enabling CFI in real systems is not straightforward, since in many cases the actual Control-flow Graph (CFG) of a program can be only approximated. Even in the case that there is perfect knowledge of the CFG, ensuring that all return instructions will return to their actual call sites, without employing a shadow stack, is questionable. On the other hand, the community has expressed concerns related to significant overheads stemming from enabling a shadow stack. In this paper, we acknowledge the importance of a shadow stack for supporting and strengthening any CFI policy. In addition, we project that implementing a full-featured CFI-enabled Instruction Set Architecture (ISA) in actual hardware with an in-chip secure memory can be efficiently carried out and the prototype experiences negligible overheads. For supporting our case, we implement by modifying a SPARC SoC and evaluate the prototype on an FPGA board by running all SPECInt benchmarks instrumented with a fine-grained CFI policy. The evaluation shows that HCFI can effectively protect applications from code-reuse attacks, while adding less than 1% runtime overhead.
Evaluation of Cryptolepine and Huperzine Derivatives as Lead Compounds towards New Agents for the Treatment of Human African Trypanosomiasis

The alkaloid cryptolepine (1) and eight synthetic analogues (2-8) were assessed for in vitro activities against Trypanosoma brucei. Four of the analogues were found to be highly potent with IC50 values of less than 3 nM and three of these were assessed against T. brucei brucei infection in rats. The most effective compound was 2, 7-dibromocryptolepine (7); a single oral dose of 20 mg/kg suppressed parasitaemia and increased the mean survival time to 13.6 days compared with 8.4 days for untreated controls. In addition, four huperzine derivatives (9-12) were shown to have in vitro antitrypanosomal activities with IC50 values ranging from 303-377 nM.
Evaluation of tropical coastal land cover and land use changes and their impacts on ecosystem service values

ABSTRACT Understanding about land cover and land use (LCLU) changes, as well as the associated impacts on ecosystem service values (ESV) is extremely important in the management of coastal ecosystems globally. Thus, this study assessed temporal LCLU changes, the underlying socioeconomic drivers and dynamics of ESV in the coastal zone of Tanzania. The LCLU data for 2000 and 2010 were from the Globe Land 30 mapping products at 30-meter spatial resolution developed by National Geomatics Center of China, while 2016 images were produced from Landsat 8. Classification of images was done from Landsat TM/ETM+ for 2000, 2010, and 2016 years complemented with MODIS and Normalized Difference Vegetation Index time series, and Chinese HJ imagery. LCLU categories and ecosystem service coefficients were used to compute ESV on each LCLU categories. Between 2000 and 2016, farmland, shrub land, waterbody, and artificial surface expanded while forest, grazing land, and wetlands declined. The ESV increased on farmland, shrub land, and waterbody, while the decline was found on forest, grazing land, and wetlands. The ESV and the total population ratios declined from $80.4, 63.8, and $46.0 million in 2000, 2010, and 2016, respectively. Perfect positive correlation was on LCLU change and ESV, population and households in crop farming, livestock keeping, and bioenergy use. Population pressure and socioeconomic activities have amplified the degradation of the coastal ecosystems. If not abetted, there is a danger of further impairments on these ecosystems. We advise to regulate population and socioeconomic activities to avoid more negative impacts of coastal LCLU change.
How Do Judgmental Overconfidence and Overoptimism Shape Innovative Activity?

Recent field evidence suggests a positive link between overconfidence and innovative activities. In this paper we argue that the connection between overconfidence and innovation is more complex than the previous literature suggests. In particular, we show theoretically and experimentally that different forms of overconfidence may have opposing effects on innovative activity. While overoptimism is positively associated with innovation, judgmental overconfidence is negatively linked to innovation. Our results indicate that future research is well advised to take into account that the relationship between innovation and overconfidence may crucially depend on what type of overconfidence is most prevalent in a particular context.
Effect of Cerebral Perfusion Pressure on Cerebral Cortical Microvascular Shunting at High Intracranial Pressure in Rats

Background and Purpose— Recently, we showed that decreasing cerebral perfusion pressure (CPP) from 70 mm Hg to 50 mm Hg and 30 mm Hg by increasing intracranial pressure (ICP) with a fluid reservoir induces a transition from capillary (CAP) to microvascular shunt (MVS) flow in the uninjured rat brain. This transition was associated with tissue hypoxia, increased blood–brain barrier (BBB) permeability, and brain edema. Our aim was to determine whether an increase in CPP would attenuate the transition to MVS flow at high ICP. Methods— Rats were subjected to progressive, step-wise increases in ICP of up to 60 mm Hg by an artificial cerebrospinal fluid reservoir connected to the cisterna magna. CPP was maintained at 50, 60, 70, or 80 mm Hg by intravenous dopamine infusion. Microvascular red blood cell flow velocity, BBB integrity (fluorescein dye extravasation), and tissue oxygenation (nicotinamide adenine dinucleotide) were measured by in vivo 2-photon laser scanning microscopy. Doppler cortical flux, rectal and cranial temperatures, ICP, arterial blood pressure, and gases were monitored. Results— The CAP/MVS ratio increased (P<0.05) at higher ICP as CPP was increased from 50 to 80 mm Hg. At an ICP of 30 mm Hg and CPP of 50 mm Hg, the CAP/MVS ratio was 0.6±0.1. At CPP of 60, 70, and 80 mm Hg, the ratio increased to 0.9±0.1, 1.4±0.1, and 1.9±0.1, respectively (mean±SEM; P<0.05). BBB opening and increase of reduced form of nicotinamide adenine dinucleotide occurred at higher ICP as CPP was increased. Conclusions— Increasing CPP at high ICP attenuates the transition from CAP to MVS flow, development of tissue hypoxia, and increased BBB permeability.
Molecular Analysis of a Family of Arabidopsis Genes Related to Galacturonosyltransferases1[W][OA]

We are studying a Galacturonosyltransferase-Like (GATL) gene family in Arabidopsis (Arabidopsis thaliana) that was identified bioinformatically as being closely related to a group of 15 genes (Galacturonosyltransferase1 [GAUT1] to -15), one of which (GAUT1) has been shown to encode a functional galacturonosyltransferase. Here, we describe the phylogeny, gene structure, evolutionary history, genomic organization, protein topology, and expression pattern of this gene family in Arabidopsis. Expression studies (reverse transcription-polymerase chain reaction) demonstrate that all 10 AtGATL genes are transcribed, albeit to varying degrees, in Arabidopsis tissues. Promoter::β-glucuronidase expression studies show that individual AtGATL gene family members have both overlapping and unique expression patterns. Nine of the 10 AtGATL genes are expressed in all major plant organs, although not always in all cell types of those organs. AtGATL4 expression appears to be confined to pollen grains. Most of the AtGATL genes are expressed strongly in vascular tissue in both the stem and hypocotyl. Subcellular localization studies of several GATL proteins using yellow fluorescent protein tagging provide evidence supporting the Golgi localization of these proteins. Plants carrying T-DNA insertions in three AtGATL genes (atgatl3, atgatl6, and atgatl9) have reduced amounts of GalA in their stem cell walls. The xylose content increased in atgatl3 and atgatl6 stem walls. Glycome profiling of cell wall fractions from these mutants using a toolkit of diverse plant glycan-directed monoclonal antibodies showed that the mutations affect both pectins and hemicelluloses and alter overall wall structure, as indicated by altered epitope extractability patterns. The data presented suggest that the AtGATL genes encode proteins involved in cell wall biosynthesis, but their precise roles in wall biosynthesis remain to be substantiated.
The Connection between Jets, Accretion Disks, and Black Hole Mass in Blazars

The properties of relativistic radio jets are thought to be closely connected with the properties of accretion disks in active galactic nuclei. We explore this issue using a sample of 35 blazars with very long baseline observations, for which we can estimate the kinetic powers of their relativistic jets, the bolometric luminosity of their accretion disks, and the masses of their black holes. Contrary to previous claims, we find that the jet kinetic power is significantly correlated with the disk luminosity. This supports the notion that the disk is somehow coupled to the jet, even on parsec scales. Moreover, we show that the correlation improves by including the black hole mass as a second parameter. The dominance of the jet, parameterized as the ratio of the jet kinetic power to the disk luminosity, is largely controlled by and is inversely correlated with the Eddington ratio of the accretion disk. This empirical relation should serve as a useful guide for theoretical models for jet formation.
Alcohol expectancy responses from teenagers: the early forewarning signals.

BACKGROUND The Indian population is overwhelmed by the rapid developmental activities in the new millennium. This has brought in urbanization and several banes of the faster life. Alcoholism is one among the menaces which have to be tackled at an early stage. OBJECTIVE To assess the subjective expectancies from alcohol intake in young college students. METHODS We carried out a survey on the expectancy from youth of the alcohol effects, which in fact is known as the principal motivator of alcohol intake. We chose the pre-university students (n= 200; 100 males and 100 females) of one of the oldest and prestigious colleges of Mangalore (south India). The survey used the Comprehensive Effect of Alcohol (CEOA) where the students had to respond to two sets of 38 questions, in which they would mention whether they agreed or disagreed to the statement regarding the effects of alcohol intake. RESULTS From the results, we found that these young students were in agreement of the view that alcohol could cause a positive reinforcement. They also strongly agreed that alcohol consumption could cause negative effects. This was significantly more pronounced among the girls. Strikingly, only 25% of the boys and 14.5% of girls had consumed alcohol before, who indicated a stronger positive reinforce response as compared to those who had not tasted alcohol. CONCLUSIONS The results reveal that the first exposure to alcohol consumption is the key factor which leads to alcoholism. If the experience of alcohol intake and the effects of alcohol are liked with the subjects, that becomes a motivating factor for future attempts. This needs a closer look by the clinicians, counselors and the parents, who need to actively interfere in educating the youth and in guiding them in the right direction during their formative ages.
Ubiquitin-proteasome-dependent degradation of mammalian ER stearoyl-CoA desaturase

Mammalian Δ9 stearoyl-CoA desaturase 1 (SCD1) is a key enzyme in the biosynthesis of mono-unsaturated fatty acids in the endoplasmic reticulum (ER). It is a short-lived multispanning ER membrane protein, reported to be degraded by the ubiquitin-proteasome-independent pathway. We have examined SCD1 protein degradation using cultured mammalian cells. Exogenously expressed SCD1 in CHO-K1 cells was localized to the ER and turned over with a half-life of ∼3 hours. Unexpectedly, proteasome inhibitors increased the half-life of SCD1 to ∼6 hours. Endogenously expressed SCD1 in adipocyte-differentiated NIH 3T3-L1 cells was also rapidly degraded in a proteasome inhibitor-sensitive manner. In the presence of proteasome inhibitors, polyubiquitylated SCD1 accumulated in the ER and interacted with AAA-ATPase p97, which is involved in ER-associated degradation (ERAD). The 66-residue N-terminal segment carrying the PEST sequence is mainly responsible for SCD1 degradation and this segment induced instability in an otherwise stable ER membrane protein. Furthermore, SCD1 was degraded constitutively irrespective of the cellular levels of unsaturated fatty acids, which strictly regulate SCD1 gene expression. These findings indicate that the ubiquitin-proteasome-dependent ERAD system is also involved in constitutive SCD1 degradation.
Adversarial Variational Bayes: Unifying Variational Autoencoders and Generative Adversarial Networks

Variational Autoencoders (VAEs) are expressive latent variable models that can be used to learn complex probability distributions from training data. However, the quality of the resulting model crucially relies on the expressiveness of the inference model. We introduce Adversarial Variational Bayes (AVB), a technique for training Variational Autoencoders with arbitrarily expressive inference models. We achieve this by introducing an auxiliary discriminative network that allows to rephrase the maximum-likelihood-problem as a two-player game, hence establishing a principled connection between VAEs and Generative Adversarial Networks (GANs). We show that in the nonparametric limit our method yields an exact maximum-likelihood assignment for the parameters of the generative model, as well as the exact posterior distribution over the latent variables given an observation. Contrary to competing approaches which combine VAEs with GANs, our approach has a clear theoretical justification, retains most advantages of standard Variational Autoencoders and is easy to implement.
Stardust Wild 2 dust measurements

During its passage through the coma of comet 81P/Wild 2 in January 2004 to collect dust particles for return to the Earth, instruments on Stardust made extensive measurements of the dust coma environment. The inner coma was characterized by many narrow jets, imaged by the Navigation Camera. Dust fluxes measured by the Dust Flux Monitor Instrument (DFMI) revealed a highly non-uniform spatial distribution, with short duration bursts of impacts implying localized spatial density changes of orders of magnitude on scales of less than a km as well as a second period of high activity ~4000 km from the nucleus where almost 80% of the detected impacts occurred. The Cometary and Interstellar Dust Analyzer (CIDA) obtained 29 dust impact mass spectra near closest approach. The spacecraft Attitude Control System (ACS) detected one event attributable to a large particle impact. The overall mass distribution in the inner coma was dominated by the largest grains, with an average cumulative mass distribution index of α=0.75±0.05 (where the number of particles of mass m or larger, N(m)∝m). The mass distribution was consistent with the ACS detection but not with the CIDA results which implied an impact rate a factor of 10 lower. The mass distribution was also highly variable during the flyby, and during the second period of high activity, small grains dominated, with α=1.13±0.2. The enormous variations in dust spatial density over distances of a few hundred metres, have been interpreted as the result of jets and distributed particle fragmentation, with the second period of high activity resulting from outgassing and/or fragmentation of a large (10s of metres diameter) boulder. This interpretation has been received with some skepticism. We review the data, the evidence for fragmentation and refute the criticisms leveled at this interpretation. Data from other comets indicate that the same processes may have occurred and therefore may be common in comets in general.
PREDICTABILITY AND IRREVERSIBILITY OF GENETIC CHANGES ASSOCIATED WITH FLOWER COLOR EVOLUTION IN PENSTEMON BARBATUS

Two outstanding questions in evolutionary biology are whether, and how often, the genetic basis of phenotypic evolution is predictable; and whether genetic change constrains evolutionary reversibility. We address these questions by studying the genetic basis of red flower color in Penstemon barbatus. The production of red flowers often involves the inactivation of one or both of two anthocyanin pathway genes, Flavonoid 3′,5′‐hydroxylase (F3′5′h) and Flavonoid 3′‐hydroxylase (F3′h). We used gene expression and enzyme function assays to determine that redundant inactivating mutations to F3′5′h underlie the evolution of red flowers in P. barbatus. Comparison of our results to previously characterized shifts from blue to red flowers suggests that the genetic change associated with the evolution of red flowers is predictable: when it involves elimination of F3′5′H activity, functional inactivation or deletion of this gene tends to occur; however, when it involves elimination of F3′H activity, tissue‐specific regulatory substitutions occur and the gene is not functionally inactivated. This pattern is consistent with emerging data from physiological experiments indicating that F3′h may have pleiotropic effects and is thus subject to purifying selection. The multiple, redundant inactivating mutations to F3′5′h suggest that reversal to blue‐purple flowers in this group would be unlikely.
Performance Evaluation of OFDM Amplify-and-Forward Relay System with Subcarrier Permutation

We perform error probability analysis of the uncoded OFDM fixed gain Amplify-and-Forward (AF) relaying system with subcarrier permutation (SCP). Two SCP schemes, named: the best-to-best SCP (BTB SCP) and the best-to-worst SCP (BTW SCP) are considered. Closed-form expressions for the bit error rate (BER) of the above SCP methods are derived. Numerical results manifest that these SCP schemes may outperform one another, depending on the average channel conditions of the links involved. That is, BTB SCP is better at low signal-to-noise ratio (SNR) values, while BTW SCP prevails in the medium and high SNR regime. Thus, it could be concluded that OFDM AF relaying systems may switch from the BTB SCP to BTW SCP in order to achieve optimum BER performance. Moreover, using the derived end-to-end SNR probability density functions (PDF), tight upper bounds for the ergodic capacities of both SCP schemes are obtained.