gebhart/patrepeval huggingface dataset:
Phenylbutyrate Up-regulates the DJ-1 Protein and Protects Neurons in Cell Culture and in Animal Models of Parkinson Disease (2011)

Parkinson disease is caused by the death of midbrain dopamine neurons from oxidative stress, abnormal protein aggregation, and genetic predisposition. In 2003, Bonifati et al. (23) found that a single amino acid mutation in the DJ-1 protein was associated with early-onset, autosomal recessive Parkinson disease (PARK7). The mutation L166P prevents dimerization that is essential for the antioxidant and gene regulatory activity of the DJ-1 protein. Because low levels of DJ-1 cause Parkinson, we reasoned that overexpression might stop the disease. We found that overexpression of DJ-1 improved tolerance to oxidative stress by selectively up-regulating the rate-limiting step in glutathione synthesis. When we imposed a different metabolic insult, A53T mutant α-synuclein, we found that DJ-1 turned on production of the chaperone protein Hsp-70 without affecting glutathione synthesis. After screening a number of small molecules, we have found that the histone deacetylase inhibitor phenylbutyrate increases DJ-1 expression by 300% in the N27 dopamine cell line and rescues cells from oxidative stress and mutant α-synuclein toxicity. In mice, phenylbutyrate treatment leads to a 260% increase in brain DJ-1 levels and protects dopamine neurons against 1-methyl 4-phenyl 1,2,3,6-tetrahydropyridine (MPTP) toxicity. In a transgenic mouse model of diffuse Lewy body disease, long-term administration of phenylbutyrate reduces α-synuclein aggregation in brain and prevents age-related deterioration in motor and cognitive function. We conclude that drugs that up-regulate DJ-1 gene expression may slow the progression of Parkinson disease by moderating oxidative stress and protein aggregation.
Regulation of Succinate Dehydrogenase in Escherichia coli (1972)

SUMMARY: Washed suspensions of Escherichiacoli oxidized succinate when previously grown on succinate but not on glucose. A slower rateof oxidation occurred with bacteria grown with peptone as carbon source. These differences were due to alterations in the level of succinate dehydrogenase activity. Glucose repressed the biosynthesis ofthe enzyme, whereas succinate acted as specific inducer and did not increase the activity of fumarate hydratase, malate dehydrogenase or NADH dehydrogenase. Aerobic growth also increased the levels of membrane-bound succinate dehydrogenase. Induction of succinate dehydrogenase by added succinate followed the expected kinetics. Addition of glucose caused a decline in the rate of biosynthesis of succinate dehydrogenase. Succinate dehydrogenase appears to play an important respiratory role since amytal(an NADH-oxidase inhibitor) inhibited growth only slightly when succinate was used as carbon source ascompared to the strong inhibition of growth when glucose was used as carbon source.
Robust model predictive control with imperfect information (2005)

This paper presents two extensions to robust model predictive control (MPC) involving imperfect information. Previous work developed a form of MPC guaranteeing feasibility and constraint satisfaction given an unknown but bounded disturbance and perfect state information. In the first extension, this controller is modified to account for an unknown but bounded state estimation error. As an example, a simple estimator is proposed and analyzed to provide the necessary error bounds. Furthermore, it is shown that delayed state information can be handled using the same method. These analyses depend on knowledge of bounds on the measurement and disturbance uncertainties. The second extension provides a method of estimating these bounds using available data, providing an adaptive form of the controller for cases where the error levels are poorly known a priori.
Rhabdopeptide/Xenortide-like Peptides from Xenorhabdus innexi with Terminal Amines Showing Potent Antiprotozoal Activity (2018)

Seven new rhabdopeptide/xenortide-like peptides (RXPs) (1-7) with putrescine or ammonia as the C-terminal amines were isolated from Xenorhabdus innexi DSM 16336. Their chemical structures were elucidated by high-resoultion mass spectroscopy (HR-MS) and one-dimensional (1D) and two-dimensional (2D) NMR. They were evaluated for their activities against protozoan parasites and cytotoxicity against rat skeletal myoblasts (L6 cells). All tested compounds exhibited strong effects against Trypanosoma brucei rhodesiense and Plasmodium falciparum, with IC<sub>50</sub> values of 0.07-6.25 and 0.091-3.16 μM, respectively, making them the most active RXP derivatives known to date.
Gene List for Watermelon (2003)

This is the latest version of the gene list for watermelon (Citrullus lanatus (Thunb.) Matsum. and Nakai). The watermelon genes were originally organized and summarized by Poole (1944). ). The list has been expanded by Robinson et al. (1976), the Cucurbit Gene List Committee (1979, 1982, and 1987), Henderson (1991 and 1992), Rhodes and Zhang (1995), and Rhodes and Dane (1999). The current list provides an update of the known genes of watermelon. This year, the list has 162 total mutants, grouped into seed and seedling mutants, vine mutants, flower mutants, fruit mutants, resistance mutants, protein (isozyme) mutants, DNA (RFLP and RAPD) markers, and cloned genes.
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data (2009)

Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling an approximately 32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data.
Cognitive Impairment in Schizophrenia Is the Core of the Disorder (2000)

Patients with schizophrenia exhibit an exceedingly wide range of symptoms from a variety of domains. The cardinal features are abnormal ideas (such as delusions); abnormal perceptions (such as hallucinations); formal thought disorder (as evidenced by disorganized speech); motor, volitional, and behavioral disorders; and emotional disorders (such as affective flattening or inappropriateness). In addition to these diverse, and sometimes bizarre symptoms, it has become increasingly apparent that the disorder is, to variable degrees, accompanied by a broad spectrum of cognitive impairments. This review addresses the question of whether the cognitive deficits seen in schizophrenic patients are the core features of the disorder. In other words, we explore whether schizophrenia is best characterized by symptoms or cognitive deficits (we suggest the latter) and moreover, whether there is a specific cognitive deficit profile that may assist in diagnosis. First, we discuss what the cognitive deficits are. Then we address in turn the reality, frequency, predictive validity, specificity, course and susceptibility to neuroleptic effects of these cognitive impairments. In brief, we argue that various cognitive deficits are enduring features of the schizophrenia illness, that they are not state-related and are not specific to subtypes of the illness, and, more specifically, that working memory and attention are characteristically impaired in patients with schizophrenia, irrespective of their level of intelligence. Last, we conclude that problems in these cognitive domains are at the very core of the dysfunction in this disease.
Partial Cosegregation of Familial Hemiplegic Migraine and a Benign Familial Infantile Epileptic Syndrome (1997)

We describe a "benign familial infantile epileptic syndrome" with attacks of FHM at a later age. Further genetic studies in this family may help to unravel the genetic basis of epilepsy or migraine or both.
Mutations in myostatin (GDF8) in Double-Muscled Belgian Blue and Piedmontese Cattle (1997)

A visibly distinct muscular hypertrophy (mh), commonly known as double muscling, occurs with high frequency in the Belgian Blue and Piedmontese cattle breeds. The autosomal recessive mh locus causing double-muscling condition in these cattle maps to bovine chromosome 2 within the same interval as myostatin, a member of the TGF-beta superfamily of genes. Because targeted disruption of myostatin in mice results in a muscular phenotype very similar to that seen in double-muscled cattle, we have evaluated this gene as a candidate gene for double-muscling condition by cloning the bovine myostatin cDNA and examining the expression pattern and sequence of the gene in normal and double-muscled cattle. The analysis demonstrates that the levels and timing of expression do not appear to differ between Belgian Blue and normal animals, as both classes show expression initiating during fetal development and being maintained in adult muscle. Moreover, sequence analysis reveals mutations in heavy-muscled cattle of both breeds. Belgian Blue cattle are homozygous for an 11-bp deletion in the coding region that is not detected in cDNA of any normal animals examined. This deletion results in a frame-shift mutation that removes the portion of the Myostatin protein that is most highly conserved among TGF-beta family members and that is the portion targeted for disruption in the mouse study. Piedmontese animals tested have a G-A transition in the same region that changes a cysteine residue to a tyrosine. This mutation alters one of the residues that are hallmarks of the TGF-beta family and are highly conserved during evolution and among members of the gene family. It therefore appears likely that the mh allele in these breeds involves mutation within the myostatin gene and that myostatin is a negative regulator of muscle growth in cattle as well as mice.
A Note on the Inception Score (2018)

Deep generative models are powerful tools that have produced impressive results in recent years. These advances have been for the most part empirically driven, making it essential that we use high quality evaluation metrics. In this paper, we provide new insights into the Inception Score, a recently proposed and widely used evaluation metric for generative models, and demonstrate that it fails to provide useful guidance when comparing models. We discuss both suboptimalities of the metric itself and issues with its application. Finally, we call for researchers to be more systematic and careful when evaluating and comparing generative models, as the advancement of the field depends upon it.
Arabidopsis, a Model to Study Biological Functions of Isoprene Emission? (2007)

The volatile hemiterpene isoprene is emitted from plants and can affect atmospheric chemistry. Although recent studies indicate that isoprene can enhance thermotolerance or quench oxidative stress, the underlying physiological mechanisms are largely unknown. In this work, Arabidopsis (Arabidopsis thaliana), a natural nonemitter of isoprene and the model plant for functional plant analyses, has been constitutively transformed with the isoprene synthase gene (PcISPS) from Grey poplar (Populus x canescens). Overexpression of poplar ISPS in Arabidopsis resulted in isoprene-emitting rosettes that showed transiently enhanced growth rates compared to the wild type under moderate thermal stress. The findings that highest growth rates, higher dimethylallyl diphosphate levels, and enzyme activity were detected in young plants during their vegetative growth phase indicate that enhanced growth of transgenic plants under moderate thermal stress is due to introduced PcISPS. Dynamic gas-exchange studies applying transient cycles of heat stress to the wild type demonstrate clearly that the prime physiological role of isoprene formation in Arabidopsis is not to protect net assimilation from damage against thermal stress, but may instead be to retain the growth potential or coordinated vegetative development of the plant. Hence, this study demonstrates the enormous potential but also the pitfalls of transgenic Arabidopsis (or other nonnatural isoprenoid emitters) in studying isoprene biosynthesis and its biological function(s).
Shapes of atomic-hydrogen lines produced at a cathode surface (1988)

The observation of extraordinarily wide wings on the spectrum lines of atomic hydrogen in emission at the cathode surface of an electric discharge is described. Actual line shapes in pure hydrogen manifest an articulation which divides the spectrum line into three distinct regions, each arising from a separate mechanism. Several novel discharge-source configurations have been developed in preceding experimentation, these falling into the general category of hollow cathodes. Three critical experiments have been performed to elucidate the process which gives rise to the extended far wings of the hydrogen lines and to determine their physical point of origin. Ultimately, it is concluded that the cathode surface itself is essential to the mechanism for producing the extreme velocities of the excited atoms which account for the distant extended wings.
Cyclic AMP Induces Apolipoprotein E Binding Activity and Promotes Cholesterol Efflux from a Macrophage Cell Line to Apolipoprotein Acceptors (1996)

RAW 264 mouse macrophage cells were stably transfected with human apolipoprotein E (apoE) expression vectors. Clonal derivatives were characterized for expression of the human apoE2, apoE3, and apoE4 isoforms. An apoE4-expressing clonal cell line and a non-expressing clonal control cell line were loaded overnight with either [3H]cholesterol or [3H]choline. The cells were washed and incubated for 24 h in serum-free medium with or without the addition of 8-bromo-cyclic AMP (8-Br-cAMP). Only the apoE-secreting cells and only in the presence of 8-Br-cAMP released large amounts of labeled cholesterol or phosphatidylcholine into the medium. Mass analyses of cellular free and esterified cholesterol confirmed the results of the labeling studies; a decrease in cellular cholesterol content was observed in the 8-Br-cAMP-treated apoE-secreting cells, concurrent with an increase in cholesterol found in the medium. FPLC analysis of the medium demonstrated that 8-Br-cAMP treatment of the apoE-secreting cells led to an increased size fraction and amount of a peak of secreted cholesterol which comigrated with apoE. The 8-Br-cAMP-mediated increase in cholesterol efflux was also observed in non-apoE-secreting cells incubated with exogenous apoE or apoAI, and the effect of apoE was saturable. The apoE2, apoE3, and apoE4 isoforms were equally efficient in promoting 8-Br-cAMP-dependent cholesterol efflux. Reductive methylation of apoE abolished its ability to promote 8-Br-cAMP-dependent cholesterol efflux. Brefeldin A and monensin, inhibitors of protein processing through the Golgi, both blocked the 8-Br-cAMP stimulation of cholesterol efflux to exogenous apoE. 8-Br-cAMP induced specific apoE and apoAI binding, but not apoE degradation, by the RAW cells. We present a model wherein cAMP induces a membrane apolipoprotein receptor that does not lead to endocytosis and degradation, but instead promotes the transfer of lipids to apolipoproteins, which can then be released from the cell.
Axl and Growth Arrest–Specific Gene 6 Are Frequently Overexpressed in Human Gliomas and Predict Poor Prognosis in Patients with Glioblastoma Multiforme (2008)

In human gliomas, Axl and Gas6 are frequently overexpressed in both glioma and vascular cells and predict poor prognosis in GBM patients. Our results indicate that specific targeting of the Axl/Gas6 signaling pathway may represent a potential new approach for glioma treatment.
The KidsRoom (2000)

The KidsRoom is a fully automated and interactive narrative playspace for children developed at the MIT Media Laboratory. Built to explore the design of perceptually based interactive interfaces, the KidsRoom uses computer vision action recognition simultaneously with computerized control of images, video, light, music, sound, and narration to guide children through a storybook adventure. Unlike most previous work in interactive environments, the KidsRoom does not require people in the space to wear any special clothing or hardware, and the KidsRoom can accommodate up to four people simultaneously. The system was designed to use computational perception to keep most interaction in the real, physical space even as participants interacted with virtual characters and scenes.
Mer receptor tyrosine kinase promotes invasion and survival in glioblastoma multiforme (2012)

The infiltration of glioma cells into adjacent tissue is one of the major obstacles in the therapeutic management of malignant brain tumours, in most cases precluding complete surgical resection. Consequently, malignant glioma patients almost invariably experience tumour recurrences. Within the brain, glioma cells migrate rapidly either amoeboidly or mesenchymally to invade surrounding structures, in dependence on the extracellular environment. In addition, radiotherapy, frequently applied as adjuvant therapeutic modality, may enhance tumour cell mobility. Here, we show that the receptor tyrosine kinase Mer (MerTK) is overexpressed in glioblastoma multiforme (GBM) and that this is accompanied with increased invasive potential. MerTK expression is maintained in primary GBM-derived tumour spheres under stem cell culture conditions but diminishes significantly in serum-containing cultures with concomitant downregulation of Nestin and Sox2. Depletion of MerTK disrupts the rounded morphology of glioma cells and decreases their invasive capacity. Furthermore, the expression and phosphorylation of myosin light chain 2 are strongly associated with MerTK activity, indicating that the effect of MerTK on glioma cell invasion is mediated by actomyosin contractility. Finally, DNA damage robustly triggers the upregulation and phosphorylation of MerTK, which protects cells from apoptosis. This effect is strongly impaired upon MerTK depletion or overexpression of an inactive MerTK mutant. Collectively, our data suggests that MerTK is a novel therapeutic target in the treatment of the malignant gliomas.
Neural representation of verb meaning: An fMRI study (2001)

The neural basis for verb comprehension has proven elusive, in part because of the limited range of verb categories that have been assessed. In the present study, 16 healthy young adults were probed for the meaning associated with verbs of MOTION and verbs of COGNITION. We observed distinct patterns of activation for each verb subcategory: MOTION verbs are associated with recruitment of left ventral temporal-occipital cortex, bilateral prefrontal cortex and caudate, whereas COGNITION verbs are associated with left posterolateral temporal activation. These findings are consistent with the claim that the neural representations of verb subcategories are distinct. Although the "sensory-motor" hypothesis may play a role in explaining activation associated with MOTION verbs, the left posterolateral temporal distribution of cortical activation associated with COGNITION verbs cannot be easily explained by the "sensory-motor" hypothesis. We suggest that left posterolateral temporal activation supports aspects of lexical semantic processing concerned with the neural representation of propositional knowledge contributing to COGNITION verbs.
Functional Requirements for Specific Ligand Recognition by a Biotin-Binding RNA Pseudoknot (1998)

Ligand-binding RNAs and DNAs (aptamers) isolated by in vitro selection from random sequence pools provide convenient model systems for understanding the basic relationships between RNA structure and function. We describe a series of experiments that define the functional requirements for an RNA motif that specifies high-affinity binding to the carboxylation cofactor biotin. A simple pseudoknot containing an adenosine-rich loop accounts for binding in all independently derived aptamers selected to bind biotin, suggesting that it alone represents a global optimum for recognition of this particular nonaromatic, electrostatically neutral ligand. In contrast to virtually all previously identified aptamers, unpaired nucleotides make up a small fraction of the binding motif. Instead, the identity of 14 nucleotides involved in base pairing is highly conserved among functional clones and their substitution by nonidentical base pairs significantly reduces or eliminates binding. Chemical probing is consistent with the predicted pseudoknot motif and indicates that relatively little change in structure accompanies ligand binding, a strong contrast with results for other aptamers. Competition experiments suggest that the aptamer recognizes all parts of the biotin ligand, including its thiophane ring and fatty acid tail. Two alternative modes of binding are suggested by a three-dimensional model of the pseudoknot, both of which entail significant interactions with base-paired nucleotides.
Therapeutic prospects for migraine: Can paradise be regained? (2013)

Migraine is a common, complex brain disorder whose biology is becoming better understood. Despite being the most disabling of the neurological disorders on a worldwide basis, headache disorders broadly, and migraine in particular, have poor research funding and a limited academic base. Given a modicum of investment, new targets, such as calcitonin gene-related peptide-based mechanisms, and entirely novel neuromodulation approaches illustrate that much can be done to improve patient care. Genetics and neuroimaging combined with excellent clinical phenotyping and translational neuroscience approaches are set to transform life for a cohort of patients with these common brain disorders.
Rationale for a natural products approach to herbicide discovery (2012)

Weeds continue to evolve resistance to all the known modes of herbicidal action, but no herbicide with a new target site has been commercialized in nearly 20 years. The so-called 'new chemistries' are simply molecules belonging to new chemical classes that have the same mechanisms of action as older herbicides (e.g. the protoporphyrinogen-oxidase-inhibiting pyrimidinedione saflufenacil or the very-long-chain fatty acid elongase targeting sulfonylisoxazoline herbicide pyroxasulfone). Therefore, the number of tools to manage weeds, and in particular those that can control herbicide-resistant weeds, is diminishing rapidly. There is an imminent need for truly innovative classes of herbicides that explore chemical spaces and interact with target sites not previously exploited by older active ingredients. This review proposes a rationale for a natural-products-centered approach to herbicide discovery that capitalizes on the structural diversity and ingenuity afforded by these biologically active compounds. The natural process of extended-throughput screening (high number of compounds tested on many potential target sites over long periods of times) that has shaped the evolution of natural products tends to generate molecules tailored to interact with specific target sites. As this review shows, there is generally little overlap between the mode of action of natural and synthetic phytotoxins, and more emphasis should be placed on applying methods that have proved beneficial to the pharmaceutical industry to solve problems in the agrochemical industry.