Miracle-dz/UniFAR-FTUs huggingface dataset:
Transition from Natively Unfolded to Folded State Induced by Desiccation in an Anhydrobiotic Nematode Protein*

Late embryogenesis abundant (LEA) proteins are associated with desiccation tolerance in resurrection plants and in plant seeds, and the recent discovery of a dehydration-induced Group 3 LEA-like gene in the nematode Aphelenchus avenae suggests a similar association in anhydrobiotic animals. Despite their importance, little is known about the structure of Group 3 LEA proteins, although computer modeling and secondary structure algorithms predict a largely α-helical monomer that forms coiled coil oligomers. We have therefore investigated the structure of the nematode protein, AavLEA1, in the first such analysis of a well characterized Group 3 LEA-like protein. Immunoblotting and subunit cross-linking experiments demonstrate limited oligomerization of AavLEA1, but analytical ultracentrifugation and gel filtration show that the vast majority of the protein is monomeric. Moreover, CD, fluorescence emission, and Fourier transform-infrared spectroscopy indicate an unstructured conformation for the nematode protein. Therefore, in solution, no evidence was found to support structure predictions; instead, AavLEA1 seems to be natively unfolded with a high degree of hydration and low compactness. Such proteins can, however, be induced to fold into more rigid structures by partner molecules or by altered physiological conditions. Because AavLEA1 is associated with desiccation stress, its Fourier transform-infrared spectrum in the dehydrated state was examined. A dramatic but reversible increase in α-helix and, possibly, coiled coil formation was observed on drying, indicating that computer predictions of secondary structure may be correct for the solid state. This unusual finding offers the possibility that structural shifts in Group 3 LEA proteins occur on dehydration, perhaps consistent with their role in anhydrobiosis.
Adaptive Evolution of the Chlamydia trachomatis Dominant Antigen Reveals Distinct Evolutionary Scenarios for B- and T-cell Epitopes: Worldwide Survey

Background Chlamydia trachomatis is one of the most disseminated human pathogens, for which no vaccine is available yet. Understanding the impact of the host pressure on pathogen antigens is crucial, but so far it was only assessed for highly-restricted geographic areas. We aimed to evaluate the evolutionary picture of the chlamydial key antigen (MOMP), which is one of the leading multi-subunit vaccine candidates, in a worldwide basis. Methodology/Principal Findings Using genetics, molecular evolution methods and mathematical modelling, we analyzed all MOMP sequences reported worldwide, composed by 5026 strains from 33 geographic regions of five continents. Overall, 35.9% of variants were detected. The evolutionary pattern of MOMP amino acid gains/losses was found to differ from the remaining chromosome, reflecting the demanding constraints of this porin, adhesin and dominant antigen. Amino acid changes were 4.3-fold more frequent in host-interacting domains (P<10−12), specifically within B-cell epitopes (P<10−5), where 25% of them are at fixation (P<10−5). According to the typical pathogen-host arms race, this rampant B-cell antigenic variation likely represents neutralization escape mutants, as some mutations were previously shown to abrogate neutralization of chlamydial infectivity in vitro. In contrast, T-cell clusters of diverse HLA specificities are under purifying selection, suggesting a strategy that may lead to immune subversion. Moreover, several silent mutations are at fixation, generating preferential codons that may influence expression, and may also reflect recombination-derived ‘hitchhiking-effect’ from favourable nonsilent changes. Interestingly, the most prevalent C. trachomatis genotypes, E and F, showed a mutation rate 22.3-fold lower than that of the remainder (P<10−20), suggesting more fitted antigenic profiles. Conclusions/Significance Globally, the adaptive evolution of the C. trachomatis dominant antigen is likely driven by its complex pathogenesis-related function and reflects distinct evolutionary antigenic scenarios that may benefit the pathogen, and thus should be taking into account in the development of a MOMP-based vaccine.
Coordinated Control with Obstacle Avoidance for Robot Manipulators

This thesis addresses the problem of robot synchronization with obstacle avoidance. While these two fields have been studied extensively on their own, they have not yet been considered together as one problem. This thesis is divided roughly into four parts which are to some extent self contained. The theory is presented in a narrative that culminates with the stability proof of the proposed controller. Examples and figures are used in order to keep the material manageable and readable. The introductory part of the thesis consists of chapters 1 and 2. We present the notation and some mathematical background which is necessary for the theoretical analysis. We go on to review the diversity of ways in which one may approach this problem from a control design standpoint. We derive the robot dynamical model in chapter 3 as well as solve other modeling specific problems. This chapter is of little theoretical interest, but is needed to implement a simulator on which we may test our controller. This chapter contains no new contributions but can be read as a guide to robot modeling. The first contributions in this thesis are found in chapter 4 where we propose a real time implementable solution for solving the shortest distance estimation problem. It is important to know the distance to an obstacle in order to avoid it. The solution is a dynamic implementation of a steepest descent optimization scheme which is suitable to run on-line. Chapter 5 is an introduction to the involved control design found in chapter 6. We review results from obstacle avoidance literature and argue for our choice of using the task space control design method. The main contribution of this thesis is found in chapter 6. A controller is developed and is shown to produce a stable closed loop system. We first develop a controller considering only collision for the end effector, and then we extend this to work with full robot collision. The response of the robot is such that it will track a reference trajectory whenever it is locally possible. When one cannot track the reference trajectory because of obstacles hindering the movement, then the trajectory is tracked in all directions in which the robot can move freely. The controller is simple and elegant, and does not rely on heuristics common in traditional solutions to obstacle avoidance control.
Quantitative phytochemical profile of the leaves of Cissus populnea Guill. and Perr. (Vitaceae) â an important medicinal plant in central Nigeria

Phytochemical analysis was conducted on the leaves of Cissus populnea Guill. & Perr. , a plant belonging to the family- Vitaceae/Ampelidaceae. The leaves were collected from New Bussa, Niger State, Northern Nigeria, air-dried and ground into fine powder. The powdered leaves were screened and results were properly recorded as observed. Results showed that the saponin content was the highest with about 47.3%. This is followed by anthraquinones – 33.2% and flavonoid – 6.48%. Although, results also showed that the cyanogenic glycoside content (3.65%) is indicative of its poisonous property as the human body may not withstand this large amount at a time, the small quantity of alkaloid – 2.49% (0.15±0.07mg/g) also suggests that it may be harmless in some ways. This study, however, supports the fact that leaves of C. populnea contain important compounds which may be useful in medicine, it also suggests that further research should be conducted into the plant as a whole, since some of the phytochemicals may be very dangerous to the human body whether consumed as vegetable or used as medicine.
Overexpression of Heat Shock Factor Gene HsfA3 Increases Galactinol Levels and Oxidative Stress Tolerance in Arabidopsis

Heat shock factors (Hsfs) are central regulators of abiotic stress responses, especially heat stress responses, in plants. In the current study, we characterized the activity of the Hsf gene HsfA3 in Arabidopsis under oxidative stress conditions. HsfA3 transcription in seedlings was induced by reactive oxygen species (ROS), exogenous hydrogen peroxide (H2O2), and an endogenous H2O2 propagator, 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB). HsfA3-overexpressing transgenic plants exhibited increased oxidative stress tolerance compared to untransformed wild-type plants (WT), as revealed by changes in fresh weight, chlorophyll fluorescence, and ion leakage under light conditions. The expression of several genes encoding galactinol synthase (GolS), a key enzyme in the biosynthesis of raffinose family oligosaccharides (RFOs), which function as antioxidants in plant cells, was induced in HsfA3 overexpressors. In addition, galactinol levels were higher in HsfA3 overexpressors than in WT under unstressed conditions. In transient transactivation assays using Arabidopsis leaf protoplasts, HsfA3 activated the transcription of a reporter gene driven by the GolS1 or GolS2 promoter. Electrophoretic mobility shift assays showed that GolS1 and GolS2 are directly regulated by HsfA3. Taken together, these findings provide evidence that GolS1 and GolS2 are directly regulated by HsfA3 and that GolS enzymes play an important role in improving oxidative stress tolerance by increasing galactinol biosynthesis in Arabidopsis.
Recurrence in early gastric cancer--presence of micrometastasis in lymph node of node negative early gastric cancer patient with recurrence.

BACKGROUND/AIMS There are cases of recurrence even after curative resection in early gastric cancer. METHODOLOGY Seven hundred and sixty-five patients with early gastric cancer who underwent curative gastrectomy were analyzed to identify the prognostic factor. Micrometastases within lymph nodes were determined by immunohistochemistry using anti-cytokeratin antibody in node-negative early gastric cancer patients with recurrence. RESULTS The recurrence was observed in 17 patients. Hematogenous recurrence was observed most frequently (47.1%), followed by peritoneal recurrence (23.5%). Of 17 patients with recurrence, 6 (35.3%) patients died more than 5 years after operation. The prognosis was poorer when the patients were older, and the depth of invasion was greater, lymph node metastasis, lymphatic involvement, and vascular involvement were present, and lymph node dissection was limited. The independent prognostic factors were lymph node metastasis, lymph node dissection, and age by multivariate analysis using Cox proportional hazards. Micrometastases within lymph nodes were confirmed in 3 of 6 node-negative patients with recurrence. CONCLUSIONS When patients have lymph node metastases or are older, close and long-term follow-up and careful planning of postoperative adjuvant therapy might be necessary to avoid recurrence. The detection of micrometastases by anti-cytokeratin antibody might be useful for predicting the possibility of recurrence in early gastric cancer.
A behaviorally related developmental switch in nitrergic modulation of locomotor rhythmogenesis in larval Xenopus tadpoles

Locomotor control requires functional flexibility to support an animal's full behavioral repertoire. This flexibility is partly endowed by neuromodulators, allowing neural networks to generate a range of motor output configurations. In hatchling Xenopus tadpoles, before the onset of free-swimming behavior, the gaseous modulator nitric oxide (NO) inhibits locomotor output, shortening swim episodes and decreasing swim cycle frequency. While populations of nitrergic neurons are already present in the tadpole's brain stem at hatching, neurons positive for the NO-synthetic enzyme, NO synthase, subsequently appear in the spinal cord, suggesting additional as yet unidentified roles for NO during larval development. Here, we first describe the expression of locomotor behavior during the animal's change from an early sessile to a later free-swimming lifestyle and then compare the effects of NO throughout tadpole development. We identify a discrete switch in nitrergic modulation from net inhibition to overall excitation, coincident with the transition to free-swimming locomotion. Additionally, we show in isolated brain stem-spinal cord preparations of older larvae that NO's excitatory effects are manifested as an increase in the probability of spontaneous swim episode occurrence, as found previously for the neurotransmitter dopamine, but that these effects are mediated within the brain stem. Moreover, while the effects of NO and dopamine are similar, the two modulators act in parallel rather than NO operating serially by modulating dopaminergic signaling. Finally, NO's activation of neurons in the brain stem also leads to the release of NO in the spinal cord that subsequently contributes to NO's facilitation of swimming.
Building Code with Dynamic Staging

When creating a new domain-specific language (DSL) it is common to embed it as a part of a flexible host language, rather than creating it entirely from scratch. The semantics of an embedded DSL (EDSL) is either given directly as a set of functions (shallow embedding), or an AST is constructed that is later processed (deep embedding). Typically, the deep embedding is used when the EDSL specifies domain-specific optimizations (DSO) in a form of AST transformations. In this paper we show that deep embedding is not necessary to specify most optimizations. We define language semantics as action functions that are executed during parsing. These actions build incrementally a new, arbitrary complex program function. The EDSL designer is able to specify many aspects of the semantics as a runnable code, such as variable scoping rules, custom type checking, arbitrary control flow structures, or DSO. A sufficiently powerful staging mechanism helps assembling the code from different actions, as well as evaluate the semantics in arbitrarily many stages. In the end, we obtain code that is as efficient as one written by hand. We never create any object representation of the code. No external traversing algorithm is used to process the code. All program fragments are functions with their entire semantics embedded within the function bodies. This approach allows reusing the code between EDSL and the host language, as well as combining actions of many different EDSLs.
Thesauruses for Prepositional Phrase Attachment

Probabilistic models have been effective in resolving prepositional phrase attachment ambiguity, but sparse data remains a significant problem. We propose a solution based on similarity-based smoothing, where the probability of new PPs is estimated with information from similar examples generated using a thesaurus. Three thesauruses are compared on this task: two existing generic thesauruses and a new specialist PP thesaurus tailored for this problem. We also compare three smoothing techniques for prepositional phrases. We find that the similarity scores provided by the thesaurus tend to weight distant neighbours too highly, and describe a better score based on the rank of a word in the list of similar words. Our smoothing methods are applied to an existing PP attachment model and we obtain significant improvements over the baseline.
Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

Associating genetic variation with quantitative measures of gene regulation offers a way to bridge the gap between genotype and complex phenotypes. In order to identify quantitative trait loci (QTLs) that influence the binding of a transcription factor in humans, we measured binding of the multifunctional transcription and chromatin factor CTCF in 51 HapMap cell lines. We identified thousands of QTLs in which genotype differences were associated with differences in CTCF binding strength, hundreds of them confirmed by directly observable allele-specific binding bias. The majority of QTLs were either within 1 kb of the CTCF binding motif, or in linkage disequilibrium with a variant within 1 kb of the motif. On the X chromosome we observed three classes of binding sites: a minority class bound only to the active copy of the X chromosome, the majority class bound to both the active and inactive X, and a small set of female-specific CTCF sites associated with two non-coding RNA genes. In sum, our data reveal extensive genetic effects on CTCF binding, both direct and indirect, and identify a diversity of patterns of CTCF binding on the X chromosome.
Development of a Pseudotyped-Lentiviral-Vector-Based Neutralization Assay for Chikungunya Virus Infection

ABSTRACT Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes chikungunya fever in Africa, South Asia, and Southeast Asia. Because the mosquito vector Aedes albopictus is present in habitats across Europe, North America, and East Asia, CHIKV has become a serious worldwide public health concern. Infection with CHIKV typically causes fever, rash, myalgia, and arthralgia. One of the important questions yet to be answered is how the host immune system is involved in the development of this disease. In this study, we prepared a CHIKV-pseudotyped lentiviral vector for use in a safe and convenient neutralization (NT) assay and analyzed its efficacy. The CHIKV-pseudotyped lentiviral vector was prepared by cotransfection with plasmids encoding the CHIKV glycoproteins E3, E2, 6k, and E1, packaging elements, and a luciferase reporter. This alternative to native CHIKV can be safely handled in a biosafety level 2 facility. The NT assay was optimized using sera from CHIKV-immunized mice and then applied to human patient sera. The majority of the serum samples from patients with chikungunya in Thailand showed robust neutralization activities, with titers that were tightly correlated with those determined by a conventional NT assay. Moreover, there was a strong correlation with the CHIKV antibody titers as determined by enzyme-linked immunosorbent assay. Thus, the CHIKV-pseudotyped-lentiviral-vector-based NT assay system is a powerful tool for examining the neutralization activity of patient sera, which will lead to a better understanding of the immune responses involved in CHIKV infection.
Clinical Management of Metabolic Syndrome: Report of the American Heart Association/National Heart, Lung, and Blood Institute/American Diabetes Association Conference on Scientific Issues Related to Management

The National Cholesterol Education Program’s Adult Treatment Panel III report (ATP III)1 identified the metabolic syndrome as a multiplex risk factor for cardiovascular disease (CVD) that is deserving of more clinical attention. Subsequently, the National Heart, Lung, and Blood Institute (NHLBI), in collaboration with the American Heart Association (AHA), convened a conference to examine scientific issues related to definition of the metabolic syndrome.2 The present report summarizes a second conference devoted to clinical management of the metabolic syndrome, which was sponsored by the AHA in partnership with the NHLBI and cosponsored by the American Diabetes Association (ADA). This latter conference considered the following issues: (1) pathogenesis and presentation of the metabolic syndrome, (2) management of underlying risk factors, (3) management of metabolic risk factors, and (4) unresolved issues and research challenges. The conference on definition2 confirmed CVD as a major clinical outcome of metabolic syndrome and identified 6 major components of the syndrome: abdominal obesity, atherogenic dyslipidemia, elevated blood pressure, insulin resistance ± glucose intolerance, a proinflammatory state, and a prothrombotic state. The follow-up conference on management was structured around therapies for these components. Clinical recognition of the metabolic syndrome is generally based on finding several well-recognized signs in clinical practice: abdominal obesity, elevated triglycerides, reduced HDL cholesterol, raised blood pressure, and elevated plasma glucose. In addition, research shows that other components not routinely measured commonly aggregate with the major components: elevated apolipoprotein B, small LDL particles, insulin resistance and hyperinsulinemia, impaired glucose tolerance (IGT), elevated C-reactive protein (CRP), and variation in coagulation factors (eg, plasminogen activator inhibitor [PAI]-1 and fibrinogen). The conference on definition2 also emphasized that risk for type 2 diabetes is higher in persons with metabolic syndrome and that diabetes is a major risk factor for CVD. It also examined various criteria for …
Exploiting fullwaveform lidar signals to estimate timber volume and above-ground biomass of individual trees

Volume and biomass are estimated mostly using tree diameter at breast height (BDH), which is not reachable using light detection and ranging (lidar) data. In this paper, we compare volume and biomass estimations performed using lidar metrics derived from a traditional canopy height model (CHM), such as total height and crown area, with estimations using additional metrics derived from fullwaveform (FW) lidar signals related to the vertical distribution of vegetation. The study is performed on a selection of black pine trees (Pinus nigra ssp. nigra [Arn.]) in the French Alps. Predictive models are built on CHM-only and CHM+FW metrics, automatically selected using a stepwise algorithm, and the accuracy of the different models is compared. We find that FW metrics improve volume estimation of 3% and biomass estimations from 5% to 7%, with a slightly less spread distribution error.
Perspective Distortion from Interpersonal Distance Is an Implicit Visual Cue for Social Judgments of Faces

The basis on which people make social judgments from the image of a face remains an important open problem in fields ranging from psychology to neuroscience and economics. Multiple cues from facial appearance influence the judgments that viewers make. Here we investigate the contribution of a novel cue: the change in appearance due to the perspective distortion that results from viewing distance. We found that photographs of faces taken from within personal space elicit lower investments in an economic trust game, and lower ratings of social traits (such as trustworthiness, competence, and attractiveness), compared to photographs taken from a greater distance. The effect was replicated across multiple studies that controlled for facial image size, facial expression and lighting, and was not explained by face width-to-height ratio, explicit knowledge of the camera distance, or whether the faces are perceived as typical. These results demonstrate a novel facial cue influencing a range of social judgments as a function of interpersonal distance, an effect that may be processed implicitly.