gebhart/patrepeval huggingface dataset:
Gut microbiome skin axis in the development of atopic dermatitis. (2021)

Atopic dermatitis mostly starts with children in early life. Besides the aetiological factors, like environmental, dietary or medical exposures, gut-skin axis microbiome studies have an impact to investigate and to understand the relation between the gut microbiome and changes to the skin microbiom as well as resulting skin diseases like atopic dermatitis. Infants start forming their microbiome in early life and some studies suggest that this phase has a crucial role in AD development. Balanced bacterial composition is important to maintain healthy skin as the gut microbiome dysbiosis may result in dramatic shifting in the skin microbiome that gives better chance for some bacteria, such as staphylococcus aureus, to prevail which has been reported to contribute to AD development. Among several factors, immunological activity has a strong relation to microbiome, changed composition and AD development. Supplements of prebiotic and probiotic could be a positive treatment approach. More studies regarding the gut-skin axis microbiome in general and diseases associated with microbiome, such as AD, are needed.
Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis (2020)

Chemical tools to monitor drug-target engagement of endogenously expressed protein kinases are highly desirable for preclinical target validation in drug discovery. Here, we describe a chemical genetics strategy to selectively study target engagement of endogenous kinases. By substituting a serine residue into cysteine at the DFG-1 position in the ATP-binding pocket, we sensitize the non-receptor tyrosine kinase FES towards covalent labeling by a complementary fluorescent chemical probe. This mutation is introduced in the endogenous FES gene of HL-60 cells using CRISPR/Cas9 gene editing. Leveraging the temporal and acute control offered by our strategy, we show that FES activity is dispensable for differentiation of HL-60 cells towards macrophages. Instead, FES plays a key role in neutrophil phagocytosis via SYK kinase activation. This chemical genetics strategy holds promise as a target validation method for kinases.
Engineering Antibodies for Cancer Therapy (2011)

The advent of modern antibody engineering has led to numerous successes in the application of these proteins for cancer therapy in the 13 years since the first Food and Drug Administration approval, which has stimulated active interest in developing more and better drugs based on these molecules. A wide range of tools for discovering and engineering antibodies has been brought to bear on this challenge in the past two decades. Here, we summarize mechanisms of monoclonal antibody therapeutic activity, challenges to effective antibody-based treatment, existing technologies for antibody engineering, and current concepts for engineering new antibody formats and antibody alternatives as next generation biopharmaceuticals for cancer treatment.
Implementation of pulsed-latch and pulsed-register circuits to minimize clocking power (2011)

A pulsed-latch can be modeled as a fast flip-flop. This allows conventional flip-flop designs to be migrated to pulsed-latch versions by simple replacement to reduce the clocking power. A key step in the migration process is to insert pulsers, which generate clock pulse to drive local latches; the number of pulsers as well as the wirelength of clock routing must be minimized to reduce the clocking power. We formulate a pulser insertion problem to find a set of latch groups where each group shares a pulser and its load constraint is satisfied; both an ILP formulation and a heuristic algorithm are presented to solve the problem. Experimental results of circuits implemented with 32-nm CMOS technology show that the clocking power of pulsed-latch designs obtained by our approach is 5.9% less than that of greedy approach; this is 44.7% less than that of flip-flop designs. We also consider the problem of pulsed-register where a pulser is integrated with multiple latches. A concept of logical distance is explored during our clustering algorithm to minimize the overhead of signal wirelength when converting flip-flops to pulsed-registers. Compared with flip-flop circuits, signal wirelength is increased by 6.3%, which is 1.4% smaller than without considering logical distance, while reducing the clocking power by 24%.
Multi-Attribute Dispatching Rules For Agv Systems With Many Vehicles (2004)

Internal transport systems using automated guided vehicles (AGVs) are widely used in many facilities such as warehouses, distribution centers and transshipment terminals. Most AGV systems use online dispatching rules to control vehicle movements. In literature, there are many types of dispatching rules such as single- and multi-attribute dispatching rules. However, a dispatching rule that is good for all cases does not exist. In this research, we study a specific type of AGV environments which has not received much attention from researchers - AGV systems with many vehicles as can be seen in airport baggage handling systems. We propose two new multi-attribute dispatching rules for this type of environment and compare their performance with that of two of the best dispatching rules in literature. Using simulation we show that the new multi-attribute dispatching rules are robust and perform very well.
Object-oriented requirements modeling based on UML (2003)

Provides research into object-oriented (OO) requirements modeling. The proposed OO modeling strategy is based on the semantics and the diagrammatic notation of UML. The semantics of UML formalizes the expression of the user requirements, while the diagrammatic notation also enhances the understandability, traceability, verifiability and modifiability of the requirements model. The ability of the system should greatly benefit the end-users and the analysts who participate in the activity of the whole requirements engineering life-cycle. To demonstrate the viability of the approach, we take an example of a small-byte subscription system.
Interpreting patient-reported outcomes from clinical trials in COPD: a discussion (2016)

Abstract: One of the challenges faced by the practising physician is the interpretation of patient-reported outcomes (PROs) in clinical trials and the relevance of such data to their patients. This is especially true when caring for patients with progressive diseases such as COPD. In an attempt to incorporate the patient perspective, many clinical trials now include assessments of PROs. These are formalized methods of capturing patient-centered information. Given the importance of PROs in evaluating the potential utility of an intervention for a patient with COPD, it is important that physicians are able to critically interpret (and critique) the results derived from them. Therefore, in this paper, a series of questions is posed for the practising physician to consider when reviewing the treatment effectiveness as assessed by PROs. The focus is on the St George’s Respiratory Questionnaire for worked examples, but the principles apply equally to other symptom-based questionnaires. A number of different ways of presenting PRO data are discussed, including the concept of the minimum clinically important difference, whether there is a ceiling effect to PRO results, and the strengths and weaknesses of responder analyses. Using a worked example, the value of including a placebo arm in a study is illustrated, and the influence of the study on PRO results is considered, in terms of the design, patient withdrawal, and the selection of the study population. For the practising clinician, the most important consideration is the importance of individualization of treatment (and of treatment goals). To inform such treatment, clinicians need to critically review PRO data. The hope is that the questions posed here will help to build a framework for this critical review. Keywords: patient-centered outcomes research, St George’s Respiratory Questionnaire, COPD, data interpretation, statistical
Transition‐Metal‐Catalyzed Denitrogenative Transannulation: Converting Triazoles into Other Heterocyclic Systems (2011)

Abstract Transition metal catalyzed denitrogenative transannulation of a triazole ring has recently received considerable attention as a new concept for the construction of diverse nitrogen‐containing heterocyclic cores. This method allows a single‐step synthesis of complex nitrogen heterocycles from easily available and cheap triazole precursors. In this Minireview, recent progress of the transition metal catalyzed denitrogenative transannulation of a triazole ring, which was discovered in 2007, is discussed.
ConExT-U: A Context-Aware Exception Handling Mechanism for Task-Based Ubiquitous Systems (2014)

Context-awareness is a central aspect in the design of ubiquitous systems, characterizing their ability to observe the environment's context changes and adapt its structure and behavior according. Since those systems can be able to make autonomous decisions (i.e., without direct user intervention), dependability becomes an important requirement. The exception handling is a well-known error recovery technique employed to improve the software robustness and contributes to the overall software system's reliability and dependability. However, despite its benefits, exception handling still not widely used in the development of ubiquitous systems. In fact, we argue that is consequence of the lack of a proper exception handling mechanism to support it during the development and execution phases. In order to address this problem, we propose a context-aware exception handling mechanism designed specifically for context-aware ubiquitous systems. The proposed mechanism is implemented as a Java-based framework that provides a task-based model for building robust ubiquitous systems. A prototype of a ubiquitous parking control system is implemented to explore and validate the features of the proposed mechanism.
Quantum Well Infrared Photodetector (QWIP) Focal Plane Arrays (1998)

Intrinsic infrared detectors in the long-wavelength range (6 - 20 ??are based on interband transition which promotes an electron across the band gap (E(sub g)) from the valence band to the conduction band.
High resolution electron energy loss spectroscopy study of vapor-deposited polyaniline thin films (1997)

Vapor deposited polyaniline films on Cu(110) have been characterized using high resolution electron energy loss spectroscopy. Ultrathin films (⩽100 Å) were found to exist in an oxidation state close to that of the starting emeraldine powder. After doping with HCl, the films exhibited plasmon excitations in the far-ir, suggesting that they are highly crystalline and possess electrical conductivities higher than those of HCl doped emeraldine films produced by wet-chemical deposition techniques. In contrast, thicker vapor-deposited films (⩾1000 Å) were found to be highly reduced, less crystalline, and exhibited electrical conductivities lower than those of the thinner films upon doping. These results suggest that the interactions of emeraldine with a metal surface can play an important role in determining the chemical, structural, and electronic properties of polyaniline films near the polymer-substrate interface.
A Universal Identifier for Computational Results (2011)

We present a discipline for verifiable computational scienti_c research. Our discipline revolves around three simple new concepts — verifiable computational result (VCR), VCR repository and Verifiable Result Identifier (VRI). These are web- and cloud-computing oriented concepts, which exploit today's web infrastructure to achieve standard, simple and automatic reproducibility in computational scientific research. The VCR discipline requires very slight modifications to the way researchers already conduct their computational research and authoring, and to the way publishers manage their content. In return, the discipline marks a significant step towards delivering on the long-anticipated promises of making scientific computation truly reproducible. A researcher practicing this discipline in everyday work produces computational scripts and word processor files that look very much like those they already produce today, but in which a few lines change very subtly and naturally. Those scripts produce a stream of verifiable results, which are the same tables, figures, charts and datasets the researcher traditionally would have produced, but which are watermarked for permanent identification by a VRI, and are automatically and permanently stored in a VCR repository. In a scientific community practicing Verifiable Computational Research, exchange of both ideas and data involves exchanging result identifiers—VRIs—rather than exchanging files. These identifiers are controlled, trusted and automatically generated strings that point to publicly available result as it was originally created by the computational process itself. When a verifiable result is included in a publication, its identifier can be used by any reader with a web browser to locate, browse and, where appropriate, re-execute the computation that produced the result. Journal readers can therefore scrutinize, dispute, understand and eventually trust these computational results, all to an extent impossible through textual explanations that constitute the core of scientific publications to date. In addition, the result identi_er can be used by subsequent computations to locate and retrieve both the published result (in graphical or numerical form) and the original datasets used by its generating computation. Colleagues can thus cite and import data into their own computations, just as traditional publications allow them to cite and import ideas. We describe an existing software implementation of the Verifiable Computational Research discipline, and argue that it solves many of the crucial problems commonly facing computer-based and computer-aided research in various scientific fields. Our system is secure, naturally adapted to large-scale and cloud computations and to modern massive data analysis, yet places effectively no additional workload on either the researcher or the publisher.
Understanding the Physiology of FGF21 (2015)

Fibroblast growth factor 21 (FGF21) is a peptide hormone that is synthesized by several organs and regulates energy homeostasis. Excitement surrounding this relatively recently identified hormone is based on the documented metabolic beneficial effects of FGF21, which include weight loss and improved glycemia. The biology of FGF21 is intrinsically complicated owing to its diverse metabolic functions in multiple target organs and its ability to act as an autocrine, paracrine, and endocrine factor. In the liver, FGF21 plays an important role in the regulation of fatty acid oxidation both in the fasted state and in mice consuming a high-fat, low-carbohydrate ketogenic diet. FGF21 also regulates fatty acid metabolism in mice consuming a diet that promotes hepatic lipotoxicity. In white adipose tissue (WAT), FGF21 regulates aspects of glucose metabolism, and in susceptible WAT depots, it can cause browning. This peptide is highly expressed in the pancreas, where it appears to play an anti-inflammatory role in experimental pancreatitis. It also has an anti-inflammatory role in cardiac muscle. Although typically not expressed in skeletal muscle, FGF21 is induced in situations of muscle stress, particularly mitochondrial myopathies. FGF21 has been proposed as a novel therapeutic for metabolic complications such as diabetes and fatty liver disease. This review aims to interpret and delineate the ever-expanding complexity of FGF21 physiology.
Absorption into fluorescence. A method to sense biologically relevant gas molecules (2010)

In this work we present an innovative optical sensing methodology based on the use of biomolecules as molecular gating nano-systems. Here, as an example, we report on the detection of analytes related to climate change. In particular, we focused our attention on the detection of nitric oxide (NO) and oxygen (O2). Our methodology builds on the possibility of modulating the excitation intensity of a fluorescent probe used as a transducer and a sensor molecule whose absorption is strongly affected by the binding of an analyte of interest used as a filter. The two simple conditions that have to be fulfilled for the method to work are: (a) the absorption spectrum of the sensor placed inside the cuvette, and acting as the recognition element for the analyte of interest, should strongly change upon the binding of the analyte and (b) the fluorescence dye transducer should exhibit an excitation band which overlaps with one or more absorption bands of the sensor. The absorption band of the sensor affected by the binding of the specific analyte should overlap with the excitation band of the transducer. The high sensitivity of fluorescence detection combined with the use of proteins as highly selective sensors makes this method a powerful basis for the development of a new generation of analytical assays. Proof-of-principle results showing that cytochrome c peroxidase (CcP) for NO detection and myoglobin (Mb) for O2 detection can be successfully used by exploiting our new methodology are reported. The proposed technology can be easily expanded to the determination of different target analytes.
XXXVI (2009)

<sc>One</sc> afternoon of the autumn of 1876, toward dusk, a young man of pleasing appearance rang at the door of a small apartment on the third floor of an old Roman house. On its being opened he enquired for Madame Merle; whereupon the servant,...
A wheat cytochrome P450 enhances both resistance to deoxynivalenol and grain yield (2018)

The mycotoxin deoxynivalenol (DON) serves as a plant disease virulence factor for the fungi Fusarium graminearum and F. culmorum during the development of Fusarium head blight (FHB) disease on wheat. A wheat cytochrome P450 gene from the subfamily CYP72A, TaCYP72A, was cloned from wheat cultivar CM82036. TaCYP72A was located on chromosome 3A with homeologs present on 3B and 3D of the wheat genome. Using gene expression studies, we showed that TaCYP72A variants were activated in wheat spikelets as an early response to F. graminearum, and this activation was in response to the mycotoxic Fusarium virulence factor deoxynivalenol (DON). Virus induced gene silencing (VIGS) studies in wheat heads revealed that this gene family contributes to DON resistance. VIGS resulted in more DON-induced discoloration of spikelets, as compared to mock VIGS treatment. In addition to positively affecting DON resistance, TaCYP72A also had a positive effect on grain number. VIGS of TaCYP72A genes reduced grain number by more than 59%. Thus, we provide evidence that TaCYP72A contributes to host resistance to DON and conclude that this gene family warrants further assessment as positive contributors to both biotic stress resistance and grain development in wheat.
Root based approaches to improving nitrogen use efficiency in plants (2009)

In the majority of agricultural growing regions, crop production is highly dependent on the supply of exogenous nitrogen (N) fertilizers. Traditionally, this dependency and the use of N-fertilizers to restore N depleted soils has been rewarded with increased plant health and yields. In recent years, increased competition for non-renewable fossil fuel reserves has directly elevated prices of N-fertilizers and the cost of agricultural production worldwide. Furthermore, N-fertilizer based pollution is becoming a serious issue for many regions where agriculture is highly concentrated. To help minimize the N footprint associated with agricultural production there is significant interest at the plant level to develop technologies which can allow economically viable production while using less applied N. To complement recent reviews examining N utilization efficiency in agricultural plants, this review will explore those strategies operating specifically at the root level, which may directly contribute to improved N use efficiencies in agricultural crops such as cereals, where the majority of N-fertilizers are used and lost to the environment. Root specific phenotypes that will be addressed in the context of improvements to N acquisition and assimilation efficiencies include: root morphology; root to shoot ratios; root vigour, root length density; and root N transport and metabolism.
Sensory–motor processing in the caudate nucleus and globus pallidas: a single-unit study in behaving primates (1980)

Monkeys were prepared for chronic recording of single neurons in the caudate nucleus (Cd) or globus pallidus (GP) during learned wrist flexion-extension movements triggered by visual and somatic sensory inputs. Almost two-thirds of GP cells and more than one-third of Cd cells modified their discharge during these tasks. Three categories of response types were observed. The first was movement related. The second type was event related, in which the cells responded to either the onset or offset of the sensory inputs regardless of the correcting movement direction. A third type combined elements of the first two categories and was termed complex. These cells responded to complex abstractions of the sensory-motor event. A latency analysis indicated that the majority of cells was not involved in initiating movements but may have participated in movement execution. The results of this experiment suggest that during voluntary movement the basal ganglia activity is correlated with motor outputs, sensory inputs, and perceptual abstractions of these sensory-motor events. As such the results are compatible with an influence by diverse regions of cerebral cortex on basal ganglia neurons during the movement control process.
Partially overlapping expression of Gata2 and Gata3 during inner ear development (2004)

Gata2 and Gata3 belong to the Gata family of transcription factors in vertebrates that bind to a consensus "GATA" DNA sequence. The Gata3 gene is one of the earliest markers for the developing mouse inner ear. Ear morphogenesis is blocked in Gata3-deficient embryos, whereas nothing was known of the role of Gata2 in mouse inner ear. Here, we have compared the expression patterns of Gata2 and Gata3 during normal inner ear development and investigated their relationship in mice where either Gata3 or Gata2 has been inactivated. The expression of the two Gata genes is highly overlapping at embryonic day (E)10.5 but becomes increasingly distinct later. Whereas Gata2 is predominantly expressed in the dorsal vestibular system, Gata3 was detected mainly in the ventral cochlear duct and ganglion. No phenotypic abnormalities were observed in the inner ear of Gata2-/- embryos before lethality at E10.5 and Gata3 expression was unchanged. In contrast, a delay and strong reduction of Gata2 expression was detected in Gata3-/- otic epithelium.
Immunochemical Screening of Pesticides (Simazine and Cypermethrin) in Orange Oil (2009)

Pesticide residue analysis in citrus oils is very important for their quality and marketing. This study assessed the reliability and sensitivity of enzyme-linked immunosorbent assays (ELISA) for simazine and cypermethrin screening in orange oil. Simazine was analyzed after extraction of the oil with methanolic phosphate buffer with a limit of quantitation (LOQ) of 40 microg/L for 1-fold and approximately 100 microg/L for 10-fold oils. Due to matrix effects the immunoanalysis of cypermethrin required hexane-acetonitrile partitioning followed by silica solid phase extraction. The method detected levels higher than 0.5 ppm (mg/L). This LOQ is lower than the U.S. EPA tolerance level (0.9 ppm) for cypermethrin in citrus oils. A good correlation (r(2) 0.99) between ELISA and LC-MS/MS was observed for the analysis of both analytes in 1-fold orange oil. Immunochemical screening can be used to reduce instrumental analysis costs by its use in preliminary orange oil screening.