gebhart/patrepeval huggingface dataset:
Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis (2017)

Genetic studies have shown essential functions of O-linked <i>N</i>-acetylglucosamine (O-GlcNAc) modification in plants. However, the proteins and sites subject to this posttranslational modification are largely unknown. Here, we report a large-scale proteomic identification of O-GlcNAc-modified proteins and sites in the model plant <i>Arabidopsis thaliana</i> Using lectin weak affinity chromatography to enrich modified peptides, followed by mass spectrometry, we identified 971 O-GlcNAc-modified peptides belonging to 262 proteins. The modified proteins are involved in cellular regulatory processes, including transcription, translation, epigenetic gene regulation, and signal transduction. Many proteins have functions in developmental and physiological processes specific to plants, such as hormone responses and flower development. Mass spectrometric analysis of phosphopeptides from the same samples showed that a large number of peptides could be modified by either O-GlcNAcylation or phosphorylation, but cooccurrence of the two modifications in the same peptide molecule was rare. Our study generates a snapshot of the O-GlcNAc modification landscape in plants, indicating functions in many cellular regulation pathways and providing a powerful resource for further dissecting these functions at the molecular level.
An integrated CT-imaging, CAD-based system for orthopedic surgery (2002)

A CAD graphics system that analyzes computed tomography (CT) scanned image slices and reconstructs 3-D images of bones for preoperative surgery planning is described. The purpose of this system is to aid an orthopedic surgeon in performing total knee replacement surgery. The first part of the system reads in the CT scan data of the patient's leg and performs image analysis. To interact with the surgeon's examination, CT images can be edited and manipulated on a high-resolution monitor for observation. The output of this image analysis is reconstructed into 3-D solid bones by the second part of the system, a 3-D graphic training system that can emulate the procedures of total knee arthroplasty. This planning system allows a surgeon to simulate the bone alignment, cutting, and implant placement before the operation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effect of targeting normal fasting glucose levels with basal insulin glargine on glycaemic variability and risk of hypoglycaemia: a randomized, controlled study in patients with early Type 2 diabetes (2009)

Treatment to target of FPG < 5.3 mmol/l with insulin glargine was not associated with significantly increased risk of hypoglycaemia. Strict control of FPG with insulin glargine was effective to control postprandial glucose excursion, but had no significant effect on sd and MAGE.
Ethiopian Banknote Recognition and Fake Detection Using Support Vector Machine (2018)

Currency recognition is an important task in numerous automated payment services and used to categorize the banknotes of different nation. The importance of automatic methods for currency recognition has been increasing in the time being because of circulation of fake notes is increased in today's economy. This recognition system contains basic image processing techniques such like image acquisition, image preprocesses, extract features and classification using support vector machine. Basically camera or scanner used for image acquisition. The images of currency processed using a variety of preprocessing techniques and different features of the image extracted using local binary pattern technique, once the features are extracted it is important to recognize the currency using effective classifier called Support vector machine and Finally a prototype able to recognize Ethiopian paper currency with accuracy of 98% shows high performance classification model for paper currency recognition and also verify the validity of given banknotes with average accuracy of 93% rate.
The abundance of health-associated bacteria is altered in PAH polluted soils—Implications for health in urban areas? (2017)

Long-term exposure to polyaromatic hydrocarbons (PAHs) has been connected to chronic human health disorders. It is also well-known that i) PAH contamination alters soil bacterial communities, ii) human microbiome is associated with environmental microbiome, and iii) alteration in the abundance of members in several bacterial phyla is associated with adverse or beneficial human health effects. We hypothesized that soil pollution by PAHs altered soil bacterial communities that had known associations with human health. The rationale behind our study was to increase understanding and potentially facilitate reconsidering factors that lead to health disorders in areas characterized by PAH contamination. Large containers filled with either spruce forest soil, pine forest soil, peat, or glacial sand were left to incubate or contaminated with creosote. Biological degradation of PAHs was monitored using GC-MS, and the bacterial community composition was analyzed using 454 pyrosequencing. Proteobacteria had higher and Actinobacteria and Bacteroidetes had lower relative abundance in creosote contaminated soils than in non-contaminated soils. Earlier studies have demonstrated that an increase in the abundance of Proteobacteria and decreased abundance of the phyla Actinobacteria and Bacteroidetes are particularly associated with adverse health outcomes and immunological disorders. Therefore, we propose that pollution-induced shifts in natural soil bacterial community, like in PAH-polluted areas, can contribute to the prevalence of chronic diseases. We encourage studies that simultaneously address the classic "adverse toxin effect" paradigm and our novel "altered environmental microbiome" hypothesis.
A method for constructing 3D traveling routes from GPS navigation data (2012)

In this paper we present a novel algorithm for constructing 3D vector maps for off road navigation using GPS track recordings. The algorithm treats the GPS track recordings as a point cloud and performs track clustering by iteratively aggregating the point cloud. The aggregation is done by simulating attraction forces between samples forming groups of points that belong to the same trail. Next, it constructs clusters centers out of the groups and forms center-lines that connect the cluster centers to create a 3D graph representation. Graph enrichments such as junction clarification are also applied. We demonstrate the results of our algorithm on a simulated dataset of ten tracks for verification purposes and on a dataset of actual GPS tracks of mountain bike trails. An analysis of the geodetic accuracy of the algorithm solution is given using ground control points which were measured in the field.
Mycobacterium terramassiliense, Mycobacterium rhizamassiliense and Mycobacterium numidiamassiliense sp. nov., three new Mycobacterium simiae complex species cultured from plant roots (2018)

Three slowly growing mycobacteria named strain AB308, strain AB215 and strain AB57 were isolated from the tomato plant roots. The 16S rRNA and rpoB gene sequence analyses suggested that each strain was representative of one hitherto unidentified slowly-growing Mycobacterium species of the Mycobacterium simiae complex. Genome sequencing indicated that each strain contained one chromosome of 6.015-6.029 Mbp. A total of 1,197, 1,239 and 1,175 proteins were found to be associated with virulence and 107, 76 and 82 proteins were associated with toxin/antitoxin systems for strains AB308, AB215 and AB57, respectively. The three genomes encode for secondary metabolites, with 38, 33 and 46 genes found to be associated with polyketide synthases/non-ribosomal peptide synthases and nine, seven and ten genes encoding for bacteriocins, respectively. The genome of strain AB308 encodes for one questionable prophage and three incomplete prophages, while only incomplete prophages were predicted in AB215 and AB57 genomes. Genetic and genomic data indicate that strains AB308, AB215 and AB57 are each representative of a new Mycobacterium species that we respectively named Mycobacterium terramassiliense, Mycobacterium numidiamassiliense and Mycobacterium rhizamassiliense.
早産児の体重測定法 : 「包み込み」によるストレス緩和の検討 (2002)

本研究は、体重測定時に「包み込み」を行うことにより、早産児のストレスを緩和できるか否かを明らかにすることを目的とした。当施設での裸のままで保育器外へ出す体重測定法(従来法)と、児をタオルで囲い頭部以外の身体を布で覆った状態で出すという体重測定法(包み込み法)を、早産児4事例において、各方法12場面(4名×3回)を交互に行った。体重測定前の児の状態を安静とし、体重測定中・体重測定後0～5分の5分間・体重測定後6～10分の5分間の各時期を、行動学的側面(ストレスサイン・state)から比較検討し、以下の結果を得た。ストレスサインにおいては、体重測定中では14項目中7項目で有意差が認められ、体重測定後0～5分の5分間・6～10分の5分間においても体重測定中よりは少数であるが、有意差が認められた。stateにおいては、包み込み法では体重測定中に全く上昇が見られないという結果が得られた。これらより、「包み込み」は体重測定中の早産児のストレスを緩和するのに有用であると示唆された。今後もあらゆるケアにおいて、児のストレスサインを適切に読み取り、対処法を探索していく必要がある。
Pharmacological and pharmacokinetic properties of JNJ‐40411813, a positive allosteric modulator of the mGlu2 receptor (2014)

Compounds modulating metabotropic glutamate type 2 (mGlu2) receptor activity may have therapeutic benefits in treating psychiatric disorders like schizophrenia and anxiety. The pharmacological and pharmacokinetic properties of a novel mGlu2 receptor-positive allosteric modulator (PAM), 1-butyl-3-chloro-4-(4-phenyl-1-piperidinyl)-2(1H)-pyridinone (JNJ-40411813/ADX71149) are described here. JNJ-40411813 acts as a PAM at the cloned mGlu2 receptor: EC50 = 147 ± 42 nmol/L in a [(35)S]GTPγS binding assay with human metabotropic glutamate type 2 (hmGlu2) CHO cells and EC50 = 64 ± 29 nmol/L in a Ca(2+) mobilization assay with hmGlu2 G α16 cotransfected HEK293 cells. [(35)S]GTPγS autoradiography on rat brain slices confirmed PAM activity of JNJ-40411813 on native mGlu2 receptor. JNJ-40411813 displaced [(3)H]JNJ-40068782 and [(3)H]JNJ-46281222 (mGlu2 receptor PAMs), while it failed to displace [(3)H]LY341495 (a competitive mGlu2/3 receptor antagonist). In rats, JNJ-40411813 showed ex vivo mGlu2 receptor occupancy using [(3)H]JNJ-46281222 with ED50 of 16 mg/kg (p.o.). PK-PD modeling using the same radioligand resulted in an EC50 of 1032 ng/mL. While JNJ-40411813 demonstrated moderate affinity for human 5HT2A receptor in vitro (K b = 1.1 μmol/L), higher than expected 5HT2A occupancy was observed in vivo (in rats, ED50 = 17 mg/kg p.o.) due to a metabolite. JNJ-40411813 dose dependently suppressed REM sleep (LAD, 3 mg/kg p.o.), and promoted and consolidated deep sleep. In fed rats, JNJ-40411813 (10 mg/kg p.o.) was rapidly absorbed (C max 938 ng/mL at 0.5 h) with an absolute oral bioavailability of 31%. Collectively, our data show that JNJ-40411813 is an interesting candidate to explore the therapeutic potential of mGlu2 PAMs, in in vivo rodents experiments as well as in clinical studies.
Student impulses and teacher feedback The relevance of teacher feedback for the classroom discourse and students’ meaning making in teaching on socio-scientific issues (2018)

AbstractToday teachers face an increased challenge in listening to classroom discourses and students' areas of interest to let these coincides with the overall teaching purpose by feedback. Present study explore how classroom communication can be modeled to allow this. The socio-scientific-issues raised were at the same time aimed at creating relevance in the students’ social life as giving a respond to the curriculum. The data consisted of recordings from science lessons in grade 7 and 8 in Sweden. To make visible the tension that occurred between different discourses and displacement of power in the conversations, practical epistemological analysis has been made. This resulted in a categorization of five different ways the teacher is taking care of and reconnects the students’ impulses in relation to the overall purpose. Consequently, this study is offering opportunities for teachers to, in a consciously manner, reflect on different strategies for discourse feedback in teaching.
An analysis of the Australian height datum: 1971 (1992)

Abstract There has been renewed interest in geodetic datums in Australia with several groups investigating specialised aspects of old datums and desirable attributes of their replacement datums. The Australian Height Datum: 1971 was designed primarily to meet the mapping needs of the Australian community in the late sixties. The datum has been maintained through a process of checking, modification and merging in the two decades since it was formed. This process has considerably reduced local inhomogeneities especially up the Queensland coast but has not disturbed the overall character of the datum. This paper addresses problems of homogeniety and statistical reliability of levelling data that has been used to define the Australian Height Datum. The overall conclusions reached are that the datum is homogeneous at the third order standard over the network but that much of the data is not in a strong state of control at the subsection level. This lack of control has implications in any proposal for re-adjustment.
Some Parameters of Contralateral Masking (1965)

A masking tone presented to one ear produces a threshold shift in the contralateral ear within a narrow frequency range surrounding the frequency of the masker. This is true when sound transmission across the head is effectively eliminated. The effect has been studied as a function of sensation level and duration of the masking tone for various frequency differences between the masking and the masked tones. Interaural sound transmission was minimized by using insert phones. In view of the large number of parameter values, von Békésy's tracking method has been found suitable for the investigation. The obtained data are interpreted in terms of neural excitation and inhibition patterns.
Transplantation of Fetal Midbrain Dopamine Progenitors into a Rodent Model of Parkinson’s Disease (2013)

Cell therapy is a promising experimental treatment for Parkinson's disease (PD). It is based on the idea that new dopamine neurons transplanted directly into the forebrain of the patient can structurally and functionally compensate for those lost to the disease in order to restore motor function. While there is a highly active field of research focused on the development of stem cell-based procedures, fetal tissue remains the "gold standard" as a safe and reliable source of dopamine neuron progenitors capable of structural and functional integration with existing motor circuitry following transplantation. This chapter describes the basic procedures for preparation of dopamine progenitor rich cell suspensions of ventral mesencephalon as well as implantation into the unilateral 6-hydroxydopamine model of PD and assessment of functional impact according to drug-induced rotational behavior. The description assumes a basic knowledge of animal handling and stereotaxic surgical procedures in rodents.
Supplemental Video from Syntaphilin Regulates Neutrophil Migration in Cancer (2023)

&lt;p&gt;Supplemental Video&lt;/p&gt;
γ-Secretase Partitioning into Lipid Bilayers Remodels Membrane Microdomains after Direct Insertion (2020)

γ-Secretase is a multisubunit complex that catalyzes intramembranous cleavage of transmembrane proteins. The lipid environment forms membrane microdomains that serve as spatio-temporal platforms for proteins to function properly. Despite substantial advances in the regulation of γ-secretase, the effect of the local membrane lipid microenvironment on the regulation of γ-secretase is poorly understood. Here, we characterized and quantified the partitioning of γ-secretase and its substrates, the amyloid precursor protein (APP) and Notch, into lipid bilayers using solid-supported model membranes. Notch substrate is preferentially localized in the liquid-disordered (L<sub>d</sub>) lipid domains, whereas APP and γ-secretase partition as single or higher complex in both phases but highly favor the ordered phase, especially after recruiting lipids from the ordered phase, indicating that the activity and specificity of γ-secretase against these two substrates are modulated by membrane lateral organization. Moreover, time-elapse measurements reveal that γ-secretase can recruit specific membrane components from the cholesterol-rich L<sub>o</sub> phase and thus creates a favorable lipid environment for substrate recognition and therefore activity. This work offers insight into how γ-secretase and lipid modulate each other and control its activity and specificity.
Zero-Current-Switching Multilevel Modular Switched-Capacitor DC–DC Converter (2010)

This paper presents a quasi-resonant technique for multilevel modular switched-capacitor dc-dc converter (MMSCC) to achieve zero-current switching (ZCS) without increasing cost and sacrificing reliability. This ZCS-MMSCC employs stray inductance distributed in the circuit as the resonant inductor to resonate with the capacitor and provide low <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dv</i> / <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dt</i> and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">di</i> / <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dt</i> switching transition for the device. The ZCS-MMSCC does not utilize any additional components to achieve ZCS and meanwhile solves the current and voltage spike problem during the switching transition, thus leading to reliable and high-efficiency advantages over traditional MMSCC. Furthermore, the ZCS-MMSCC reduces the capacitance needed in the circuit to attain high efficiency. In this case, the bulky capacitor bank with high capacitance in a traditional MMSCC to reduce voltage difference and achieve high efficiency is no longer necessary. A 150-W four-level ZCS-MMSCC prototype has been built. Simulation and experimental results are given to demonstrate the validity and features of the proposed soft-switching switched-capacitor circuit.
Multimodal Virtual Avatars for Investigative Interviews with Children (2021)

In this article, we present our ongoing work in the field of training police officers who conduct interviews with abused children. The objectives in this context are to protect vulnerable children from abuse, facilitate prosecution of offenders, and ensure that innocent adults are not accused of criminal acts. There is therefore a need for more data that can be used for improved interviewer training to equip police with the skills to conduct high-quality interviews. To support this important task, we propose to research a training program that utilizes different system components and multimodal data from the field of artificial intelligence such as chatbots, generation of visual content, text-to-speech, and speech-to-text. This program will be able to generate an almost unlimited amount of interview and also training data. The goal of combining all these different technologies and datatypes is to create an immersive and interactive child avatar that responds in a realistic way, to help to support the training of police interviewers, but can also produce synthetic data of interview situations that can be used to solve different problems in the same domain.
Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage (2014)

The Janus Immunogenicity Score, which integrates MHC binding and TCR cross-reactivity, provides a new tool for studying immunogenicity of pathogens and may improve the selection and optimization of antigenic elements for vaccine design.
Stemming Tigrinya Words for Information Retrieval (2012)

The increasing penetration of internet into less developed countries has resulted in the increase in the number of digital documents written in many minor languages. However, many of these languages have limited resources in terms of data, language resources and computational tools. Stemming is the reduction of inflected word forms into common basic form. It is an important analysis process in information retrieval and many natural language processing applications. In highly inflected languages such as Tigrinya, stemming is not always straightforward task. In this paper we present the development of stemmer for Tigrinya words to facilitate the information retrieval. We used a hybrid approach for stemming that combines rule based stemming which removes affixes in successively applied steps and dictionary based stemming which reduces stemming errors by verifying the resulting stem based on word distance measures. The stemmer was evaluated using two sets of Tigrinya words. The results show that it achieved an average accuracy of 89.3%.
Crystal structure changes of thio-LISICON electrolytes in humid atmosphere (2023)

Sulfide electrolytes are among the most notable materials because of their high ionic conductivity and ductility. Their primary drawback is that they are sensitive to humidity and must be handled in an inert atmosphere to prevent degradation. Understanding the degradation mechanism is necessary to establish methods for overcoming it; however, whether or not it depends on the composition of the electrolytes is not yet clear. In this study, we systematically investigated the crystal structure changes in a humid atmosphere for crystalline sulfide electrolytes (thio-LISICONs). Eight thio-LISICONs, LixMS4 (x = 3–5; M = Al, Ga, Si, Ge, Sn, P, As, and Sb), were prepared using a mechanochemical process and subsequent heat treatment. The exposure behavior was observed using in situ humidity exposure X-ray diffraction (XRD). In a humid atmosphere with a dew point of −8 °C, the electrolytes, transformed into new hydrates, all except for Li5AlS4 and Li5GaS4, which did not change. Hydrated Li4MS4 (M = Si and Ge) has the same crystal structure as that of the known hydrate Li4SnS4·13H2O. The crystal structures of hydrated Li3MS4 (M = P, As, and Sb) were identical to each other but different from those of Li3AsS4·8H2O. This study revealed that the hydration behavior of the sulfide electrolytes depends on their central element groups.
NMR structure and dynamics of inhibitory repeat domain variant 12, a plant protease inhibitor from Capsicum annuum, and its structural relationship to other plant protease inhibitors (2019)

Although several plant protease inhibitors have been structurally characterized using X-ray crystallography, very few have been studied using NMR techniques. Here, we report an NMR study of the solution structure and dynamics of an inhibitory repeat domain (IRD) variant 12 from the wound-inducible Pin-II type proteinase inhibitor from <i>Capsicum annuum</i>. IRD variant 12 (IRD12) showed strong anti-metabolic activity against the Lepidopteran insect pest, <i>Helicoverpa armigera</i>. The NMR-derived three-dimensional structure of IRD12 reveals a three-stranded anti-parallel β-sheet rigidly held together by four disulfide bridges and shows structural homology with known IRDs. It is interesting to note that the IRD12 structure containing ∼75% unstructured part still shows substantial amount of rigidity of N-H bond vectors with respect to its molecular motion.Communicated by Ramaswamy H. Sarma.