gebhart/patrepeval huggingface dataset:
The Discovery of HIV as the Cause of AIDS (2003)

Progress in scientific research rarely follows a straight path. Generally it entails many unexpected meanderings with a mix of good and bad ideas good and bad luck. The discovery of the human immunodeficiency virus (HIV) as the cause of AIDS did not avoid this pattern. The story began in an unfavorable environment: during the late 1970s many people thought that epidemic diseases caused by microbes including viruses no longer posed a threat in industrialized countries. Other prevailing beliefs were that viruses did not cause any human cancers and that there was no such thing as a retrovirus that infected humans. Some of these beliefs were justified since attempts to find tumor viruses and in particular retroviruses in cancers or other diseases in humans had a troubled history and many of the groups that had the greatest expertise in the study of retroviruses had turned their efforts toward research on oncogenes. Luckily and rather amazingly however the conceptual and technical tools arrived in our hands just before the first patients with AIDS were identified in 1981. In addition there remained a few heretical or old-fashioned groups - among which were our two laboratories - that persisted in searching for retroviruses in human cancers particularly breast cancers and leukemias. This search finally paid off with the discovery of human T-cell leukemia virus types 1 and 2 (HTLV-1 and HTLV-2) the first of which was shown to cause an unusual T-cell leukemia. This discovery was made possible by 15 years of basic research on leukemogenic retroviruses in animals including the design and development of highly sensitive biochemical assays that were based on reverse transcriptase - the enzyme that is present in all retroviruses which was discovered in 1970 by Temin and Baltimore. (excerpt)
Caspase‐dependent cleavage of the mono‐ADP‐ribosyltransferase ARTD10 interferes with its pro‐apoptotic function (2013)

ADP-ribosylation is a post-translational modification that regulates various physiological processes, including DNA damage repair, gene transcription and signal transduction. Intracellular ADP-ribosyltransferases (ARTDs or PARPs) modify their substrates either by poly- or mono-ADP-ribosylation. Previously we identified ARTD10 (formerly PARP10) as a mono-ADP-ribosyltransferase, and observed that exogenous ARTD10 but not ARTD10-G888W, a catalytically inactive mutant, interferes with cell proliferation. To expand on this observation, we established cell lines with inducible ARTD10 or ARTD10-G888W. Consistent with our previous findings, induction of the wild-type protein but not the mutant inhibited cell proliferation, primarily by inducing apoptosis. During apoptosis, ARTD10 itself was targeted by caspases. We mapped the major cleavage site at EIAMD406↓S, a sequence that was preferentially recognized by caspase-6. Caspase-dependent cleavage inhibited the pro-apoptotic activity of ARTD10, as ARTD10(1-406) and ARTD10(407-1025), either alone or together, were unable to induce apoptosis, despite catalytic activity of the latter. Deletion of the N-terminal RNA recognition motif in ARTD10(257-1025) also resulted in loss of pro-apoptotic activity. Thus our findings indicate that the RNA recognition motif contributes to the pro-apoptotic effect, together with the catalytic domain. We suggest that these two domains must be physically linked to stimulate apoptosis, possibly targeting ARTD10 through the RNA recognition motif to specific substrates that control cell death. Moreover, we established that knockdown of ARTD10 reduced apoptosis in response to DNA-damaging agents. Together, these findings indicate that ARTD10 is involved in the regulation of apoptosis, and that, once apoptosis is activated, ARTD10 is cleaved as part of negative feedback regulation.
Detection of Encrypted Cryptomining Malware Connections With Machine and Deep Learning (2020)

Nowadays, malware has become an epidemic problem. Among the attacks exploiting the computer resources of victims, one that has become usual is related to the massive amounts of computational resources needed for digital currency cryptomining. Cybercriminals steal computer resources from victims, associating these resources to the crypto-currency mining pools they benefit from. This research work focuses on offering a solution for detecting such abusive cryptomining activity, just by means of passive network monitoring. To this end, we identify a new set of highly relevant network flow features to be used jointly with a rich set of machine and deep-learning models for real-time cryptomining flow detection. We deployed a complex and realistic cryptomining scenario for training and testing machine and deep learning models, in which clients interact with real servers across the Internet and use encrypted connections. A complete set of experiments were carried out to demonstrate that, using a combination of these highly informative features with complex machine learning models, cryptomining attacks can be detected on the wire with telco-grade precision and accuracy, even if the traffic is encrypted.
Detection of seizure rhythmicity by recurrences (2008)

Epileptic seizures show a certain degree of rhythmicity, a feature of heuristic and practical interest. In this paper, we introduce a simple model of this type of behavior, and suggest a measure for detecting and quantifying it. To evaluate our method, we develop a set of test segments that incorporate rhythmicity features, and present results from the application of this measure to test segments. We then analyze electrocorticogram segments containing seizures, and present two examples. Finally, we discuss the similarity of our method to techniques for detecting unstable periodic orbits in chaotic time series.
Reorganization of Istituti Fisioterapici Ospitalieri, an oncological and dermatological clinical and research center, to face the coronavirus health emergency: adopted measures and metrics of success to achieve and keep a COVID-19-free status (2020)

We hope our experience may serve as a resource to inform clinical care models in case of future epidemiological outbreaks.
What in the world is a Shahab?: Wide Coverage Named Entity Recognition for Arabic (2006)

This paper describes the development of CICEROARABIC, the first wide coverage named entity recognition (NER) system for Modern Standard Arabic. Capable of classifying 18 different named entity classes with over 85 % F, CICEROARABIC utilizes a new 800,000-word annotated Arabic newswire corpus in order to achieve high performance without the need for hand-crafted rules or morphological information. In addition to describing results from our system, we show that accurate named entity annotation for a large number of semantic classes is feasible, even for very large corpora, and we discuss new techniques designed to boost agreement and consistency among annotators over a long-term annotation effort. 1.
Asia-Pacific Investigators and Asian Enrollment in Cardiometabolic Trials (2023)

Despite a favorable trend over the past decade, Asian participants and authors from APAC remain significantly underrepresented in seminal cardiometabolic trials; barriers to trial conduct and leadership in this region must be addressed.
ADnEV (2020)

Schema matching is a process that serves in integrating structured and semi-structured data. Being a handy tool in multiple contemporary business and commerce applications, it has been investigated in the fields of databases, AI, Semantic Web, and data mining for many years. The core challenge still remains the ability to create quality algorithmic matchers, automatic tools for identifying correspondences among data concepts ( e.g. , database attributes). In this work, we offer a novel post processing step to schema matching that improves the final matching outcome without human intervention. We present a new mechanism, similarity matrix adjustment , to calibrate a matching result and propose an algorithm (dubbed ADnEV) that manipulates, using deep neural networks, similarity matrices, created by state-of-the-art algorithmic matchers. ADnEV learns two models that iteratively adjust and evaluate the original similarity matrix. We empirically demonstrate the effectiveness of the proposed algorithmic solution for improving matching results, using real-world benchmark ontology and schema sets. We show that ADnEV can generalize into new domains without the need to learn the domain terminology, thus allowing cross-domain learning. We also show ADnEV to be a powerful tool in handling schemata which matching is particularly challenging. Finally, we show the benefit of using ADnEV in a related integration task of ontology alignment.
Switched-Capacitors as Local Converters for Snake PV Modules: A Cost/Efficiency Exploration (2018)

In order to reduce the negative effect of partial shading and other sources of current mismatch within a module, smart reconfigurable modules allow altering the connections between groups of cells (cell-strings). With a proper algorithm managing these connections, we can make sure that the majority of the cells are operating close to their MPP, even when a part of the module is shaded. Such a smart reconfigurable module consists of some extra components. Switches are needed to change the interconnection scheme. Small, local converters collect power from multiple cell-strings. They step-up the voltage to reduce the current on the central bus they are connected to. At the end where we connect to the string-level bus, a module converter further regulates the voltage for the grid or the PV array. This topology was presented before where we showed that a smart reconfigurable module could recover up to 70% of the power lost to partial shading. In this paper we take a closer look at the local DC-DC converter. More precisely, we present a cost-efficiency analysis of different converter topologies. Taking into account practical limitations (economical limitations, number of components, maximum switch currents, maximum capacitance values, etc..) we estimate efficiency and projected cost. We show that Dickson pump (CR3) with 30-35m switches is the best candidate. This would result in a chip cost of about €1.5
Optically stimulated luminescence properties of Tl-doped NH4Cl transparent ceramics fabricated by SPS method (2021)

We fabricated Tl-doped NH4Cl transparent ceramics using SPS method with varying Tl concentrations (0%, 0.01%, 0.05%, 0.1%, 0.5%, and 1%) and evaluated the properties of photoluminescence (PL), radioluminescence (RL), and optically stimulated luminescence (OSL). In PL and RL spectra, Tl-doped samples exhibited two emission peaks at around 380 and 530 nm due to the 3P1→ 1S0 transitions of Tl+ and the off-center self-trapped excitons near Tl+, respectively. In the OSL spectra, Tl-doped samples exhibited an emission peak at around 350 nm due to the 3P1 → 1S0 transitions of Tl+. In the OSL dose–response function, all the samples showed a good linearity over a range of 10–10,000 mGy.
The best practices of engineering regionalization (2014)

Software and hardware engineering in international project business has been subject to regionalization efforts for several years. We describe how such a regionalization is basically organized and performed in a multi-national company, mainly active in project business in various technical domains such as electrical substations, trains or power plants. Main accent is put on experience gathered from engineering regionalization. Special focus of this contribution is on the regionalization process chosen and on the many challenges involved. It turns out that the regionalization of engineering is a process lasting for a longer time and requiring balance between all participating parties. Best practices gathered so far are presented and further envisioned research steps are shown.
Product development using process monitoring and NDE data fusion (1998)

Composite process/product development relies on both process monitoring information and nondestructive evaluation measurements for determining application suitability. In the past these activities have been performed and analyzed independently. Our present approach is to present the process monitoring and NDE data together in a data fusion workstation. This methodology leads to final product acceptance based on a combined process monitoring and NDE criteria. The data fusion work station combines process parameter and NDE data in a single workspace enabling all the data to be used in the acceptance/rejection decision process. An example application is the induction welding process, a unique joining method for assembling primary composite structure, that offers significant cost and weight advantages over traditional fasted structure. The determination of the required time, temperature and pressure conditions used in the process to achieve a complete weld is being aided by the use of ultrasonic inspection techniques. Full waveform ultrasonic inspection data is employed to evaluate the quality of spar cap to skin fit, an essential element of the welding process, and is processed to find a parameter that can be used for weld acceptance. Certification of the completed weld incorporates the data fusion methodology.
One‐Step Preparation of Multifunctional Chitosan Microspheres by a Simple Sonochemical Method (2009)

Chitosan is a biodegradable natural polymer with great potential for pharmaceutical applications due to its biocompatibility, high charge density, nontoxicity, and mucoadhesion properties. Processing techniques for the preparation of chitosan microspheres have been extensively developed since the 1980s. The present paper describes for the first time a fast and one-step process for the preparation of stable chitosan microspheres by a simple sonochemical method. The microspheres were characterized by their particle size, surface morphology, stability, and drug-entrapment efficiency. The average size of the microspheres was found to be around 1 mum with a narrow size distribution, which enabled them to be used for in vivo applications. The encapsulation of different dyes into these microspheres was readily achieved with more than 75 % efficacy by dissolving them into the organic phase before sonication. The chitosan microspheres demonstrated excellent stability toward acidic and basic conditions ranging from pH 4 to 9, thereby indicating their implementation as possible therapeutic and diagnostic agents. The stability of these microspheres appears to be contributed from intermolecular imine cross-linking in addition to other noncovalent interactions. The ability of the surface-exposed amino groups of chitosan microspheres to undergo chemical conjugation with potential drugs and/or targeting vectors was determined by their reaction with fluorescein isothiocyanate (FITC) and fluorescamine followed by confocal microscopy.
Adaptive leases: A strong consistency mechanism for the world wide web (2003)

We argue that weak cache consistency mechanisms supported by existing Web proxy caches must be augmented by strong consistency mechanisms to support the growing diversity in application requirements. Existing strong consistency mechanisms are not appealing for Web environments due to their large state space or control message overhead. We focus on the lease approach that balances these trade-offs and present analytical models and policies for determining the optimal lease duration. We present extensions to the HTTP protocol to incorporate leases and then implement our techniques in the Squid proxy cache and the Apache Web server. Our experimental evaluation of the leases approach shows that: 1) our techniques impose modest overheads even for long leases (a lease duration of 1 hour requires state to be maintained for 1030 leases and imposes an per-object overhead of a control message every 33 minutes), 2) leases yields a 138-425 percent improvement over existing strong consistency mechanisms, and 3) the implementation overhead of leases is comparable to existing weak consistency mechanisms.
Peak Demand Management on Distribution Networks using Coordinated Behind-The-Meter PV / Battery Systems: The Bruny Island Battery Trial (2016)

We introduce the Bruny Island Battery Trial, a collaborative research project which will see around 40 photovoltaic and battery systems installed on Bruny Island in Tasmania by April 2017. This fleet of battery systems will operate via a coordinated optimisation approach featuring network constraint based price signals, to alleviate network capacity problems associated with peak-demand events, which are currently solved by on-island diesel generation. Battery owners meanwhile will benefit from two income streams, derived from time-shifting for local tariff optimisation and from network support. We show, via analysis of power flow data measurements over the preceding two-year period, that peak demand on the island is characterised by early morning and early evening peaks, and as such we demonstrate that PV systems alone will only ever have inconsequential impact upon peak demand mitigation. In contrast, we demonstrate that 40 residential-sized PV / battery systems spread across the island would have reduced peak demand over the two-year period by up to 150 kW, would have reduced the number of diesel starts from 43 down to 14 and reduced generator running hours and annual diesel energy production by up to 83% and 91% respectively. Furthermore we show, by modelling the network, the extent to which voltage is able to be controlled, particularly at the extents of the network, by such a deployment of batteries. We conclude that a fleet of behind-the-meter PV / battery systems, if coordinated with network requirements in mind, is an effective alternative to traditional network solutions in addressing peak demand and in addressing voltage issues.
Temporal responses of wild-type pigmentation and RcaE-deficient strains ofFremyelladiplosiphonduring light transitions (2011)

A temporal study was conducted to evaluate the dynamic complementary chromatic adaptation (CCA) response of two Fremyella diplosiphon strains—wild-type pigmentation strain SF33 and an RcaE-deficient (ΔrcaE) strain, which lacks the photosensor that regulates CCA. SF33 and ΔrcaE cultures were monitored for 15 days after transition of green-light (GL) acclimated cultures to red light (RL) and vice versa. SF33 showed similar growth irrespective of the external light quality; however, a ΔrcaE strain grew slower than SF33 under both RL and GL. Chlorophyll a (chla) content increased in both strains over time and was not much different under RL and GL indicating that chla biosynthesis is not affected significantly by light quality or RcaE function. Phycoerythrin is the sole pigment to absorb GL, whereas several pigments, i.e., allophycocyanin, phycocyanin and chla, function under RL to drive photosynthesis. SF33 compensates for this by synthesizing a higher percentage of PE under GL. The final pigment distribution in the ΔrcaE mutant was found to be more different from SF33 under GL than under RL indicating that RcaE is needed for a transitional response to RL and RL-dependent repression of PE accumulation, yet RcaE is virtually critical for both transitioning to and a full adaptation to GL.
Expression, refolding and indirect immobilization of horseradish peroxidase (HRP) to cellulose via a phage‐selected peptide and cellulose‐binding domain (CBD) (2001)

We examined the potential immobilization of horseradish peroxidase (HRP) to cellulose with cellulose-binding domain (CBD) as a mediator, using a ligand selected from a phage-displayed random peptide library. A 15-mer random peptide library was panned on cellulose-coated plates covered with CBD in order to find a peptide that binds to CBD in its bound form. The sequence I/LHS, which was found to be an efficient binder of CBD, was fused to a synthetic gene of HRP as an affinity tag. The tagged enzyme (tHRP) was then immobilized on microcrystalline cellulose coated with CBD, thereby demonstrating the indirect immobilization of a protein to cellulose via three amino acids selected by phage display library and CBD. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd.
Supplementary Materials & Methods from Adrenal Hyperplasia and Adenomas Are Associated with Inhibition of Phosphodiesterase 11A in Carriers of <i>PDE11A</i> Sequence Variants That Are Frequent in the Population (2023)

Supplementary Materials &amp; Methods from Adrenal Hyperplasia and Adenomas Are Associated with Inhibition of Phosphodiesterase 11A in Carriers of &lt;i&gt;PDE11A&lt;/i&gt; Sequence Variants That Are Frequent in the Population
Correction (2006)

Figure 2A contained a typographical error.The right-most vertical label read 100 mM MV instead of 10 mM MV.The corrected figure appears below.
Accumulation capacitance frequency dispersion of III-V metal-insulator-semiconductor devices due to disorder induced gap states (2014)

The origin of the anomalous frequency dispersion in accumulation capacitance of metal-insulator-semiconductor devices on InGaAs and InP substrates is investigated using modeling, electrical characterization, and chemical characterization. A comparison of the border trap model and the disorder induced gap state model for frequency dispersion is performed. The fitting of both models to experimental data indicate that the defects responsible for the measured dispersion are within approximately 0.8 nm of the surface of the crystalline semiconductor. The correlation between the spectroscopically detected bonding states at the dielectric/III-V interface, the interfacial defect density determined using capacitance-voltage, and modeled capacitance-voltage response strongly suggests that these defects are associated with the disruption of the III-V atomic bonding and not border traps associated with bonding defects within the high-k dielectric.
Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data (2022)

Our results support the hypothesis that future transcriptome studies on circulative, vector-borne pathogens should be conducted at the tissue-specific level using complete, chromosomal-length genome assemblies for the most accurate understanding of pathogen-induced changes in vector gene expression.
Reduction of pTau and APP levels in mammalian brain after low-dose radiation (2021)

Brain radiation can occur from treatment of brain tumors or accidental exposures. Brain radiation has been rarely considered, though, as a possible tool to alter protein levels involved in neurodegenerative disorders. We analyzed possible molecular and neuropathology changes of phosphorylated-Tau (pTau), all-Tau forms, β-tubulin, amyloid precursor protein (APP), glial fibrillary acidic protein (GFAP), ionized calcium binding adaptor molecule 1 (IBA-1), myelin basic protein (MBP), and GAP43 in Frontal Cortex (FC), Hippocampus (H) and Cerebellum (CRB) of swine brains following total-body low-dose radiation (1.79 Gy). Our data show that radiated-animals had lower levels of pTau in FC and H, APP in H and CRB, GAP43 in CRB, and higher level of GFAP in H versus sham-animals. These molecular changes were not accompanied by obvious neurohistological changes, except for astrogliosis in the H. These findings are novel, and might open new perspectives on brain radiation as a potential tool to interfere with the accumulation of specific proteins linked to the pathogenesis of various neurodegenerative disorders.