gebhart/patrepeval huggingface dataset:
HERV-K(OLD): Ancestor Sequences of the Human Endogenous Retrovirus Family HERV-K(HML-2) (2001)

Sequences homologous to the human endogenous retrovirus (HERV) family HERV-K(HML-2) are present in all Old World primate species. A previous study showed that a central region of the HERV-K(HML-2) gag genes in Hominoidea species displays a 96-bp deletion compared to the gag genes in lower Old World primates. The more ancient HERV-K(HML-2) sequences present in lower Old World primates were apparently not conserved during hominoid evolution, as opposed to the deletion variants. To further clarify the evolutionary origin of the HERV-K(HML-2) family, we screened GenBank with the 96-bp gag-sequence characteristic of lower Old World primates and identified, to date, 10 human sequence entries harboring either full-length or partially deleted proviral structures, probably representing remnants of a more ancient HERV-K(HML-2) variant. The high degree of mutations demonstrates the long-time presence of these HERV-K(OLD) proviruses in the genome. Nevertheless, they still belong to the HML-2 family as deduced from dot matrix and phylogenetic analyses. We estimate, based on the family ages of integrated Alu elements and on long terminal repeat (LTR) divergence data, that the average age of HERV-K(OLD) proviruses is ca. 28 million years, supporting an integration time before the evolutionary split of Hominoidea from lower Old World primates. Analysis of HERV-K(OLD) LTR sequences led to the distinction of two subgroups, both of which cluster with LTRs belonging to an evolutionarily older cluster. Taken together, our data give further insight into the evolutionary history of the HERV-K(HML-2) family during primate evolution.
Pr3+ Doped Ceramic Calcium Lanthanum Sulfide for Mid-IR Laser Gain Material (2017)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text L. B. Shaw, M. Hunt, W. Kim, S. Bayya, C. Brown, S. Bowman, and J. S. Sanghera, "Pr3+ Doped Ceramic Calcium Lanthanum Sulfide for Mid-IR Laser Gain Material," in Conference on Lasers and Electro-Optics, OSA Technical Digest (online) (Optica Publishing Group, 2017), paper JTu5A.114. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
All-window profiling of concurrent executions (2008)

This paper first demonstrates the need for all-window profiling in a concurrent execution, then presents an approximate algorithm, and finally discusses related work.
Visualizing photodynamic therapy response with time-lapse OCT in an in vitro model of metastatic ovarian cancer (2010)

Ovarian epithelial cancer has a high morbidity due to its propensity to metastasize onto surfaces in the abdomen. In order to effectively treat these metastatic lesions with photodynamic therapy (PDT), it is critical to understand the detailed dynamics of the PDT response. 3D <i>in vitro</i> models of ovarian cancer are a promising system for studying the response to PDT of these lesions, as they replicate the size, appearance, and characteristics of metastatic disease observed in the clinic. An ideal approach capable of non-purturbative, 3D imaging of this model is optical coherence tomography (OCT). An ultrahigh resolution time-lapse OCT (TL-OCT) system was used to visualize the photodynamic therapeutic response in the hours and days following treatment. Tumor nodules were observed to experience rapid cell death within the first 24 hours post-treatment using benzophorphyrin derivative monoacid A (BPD), characterized by structural breakdown of the model nodules. Highly scattering bodies were observed with OCT contrast to form at the periphery of the tumor nodules. These highly scattering moieties were identified as apoptotic bodies, indicating that OCT is capable of tracking the PDT-induced apoptosis in real-time without the need for labels.
Interdomain multipath routing (2011)

While astonishingly successful, Internet is still less reliable than the phone system and supports very limited user choice and control. As many researchers observed, multipath routing is a promising paradigm to address these issues. In this thesis, we argue that multipath routing can indeed go a long way towards these goals as well as lead to a more scalable, extensible, and evolvable Internet. 
We begin by describing Yet Another Multipath Routing (YAMR) protocol that provably constructs a set of paths resilient to any one interdomain link failure. YAMR uses an efficient scheme to construct the paths and a novel failure hiding technique to further reduce the control plane overhead. 
Next, we describe Pathlet Routing, a protocol that departs from the path-vector paradigm. Pathlet routing allows ASes to advertise policy-compliant path segments called pathlets, and allows users to stitch them together, thus forming a complete path suitable for the user's particular needs. Pathlet routing greatly reduces the forwarding table size, can efficiently express a wide class of routing policies, and provide an exponential number of paths to the users. Finally, we investigate how pathlet routing can be a basis for an evolvable Internet architecture.
Techniques and tools for the verification of concurrent systems (2012)

Model checking is an automatic formal verification technique for establishing correctness of systems. It has been widely used in industry for analysing and verifying complex safety-critical systems in application domains such as avionics, medicine and computer security, where manual testing is infeasible and even minor errors could have dire consequences. In our increasingly parallelised world, concurrency has become pivotal and seamlessly woven within programming paradigms, however, extremely challenging when it comes to modelling and establishing correctness of intended behaviour. Tools for model checking concurrent systems face severe limitations due to scalability problems arising from the need to examine all possible interleavings (schedules) of executions of parallel components. Moreover, concurrency poses additional challenges to model checking, giving rise to phenomena such as nondeterminism, deadlock, livelock, etc. In this thesis we focus on adapting and developing novel model-checking techniques for concurrent systems in the setting of the process algebra CSP and its primary model checker FDR. CSP allows for a compact modelling and precise analysis of event-based concurrency, grounded on synchronous message passing as a fundamental mechanism of inter-component communication. In particular, we investigate techniques based on symbolic model checking, static analysis and abstraction, all of them exploiting the compositionality inherent in CSP and targeting to increase the scale of systems that can be tractably analysed. Firstly, we investigate symbolic model-checking techniques based on Boolean satisfiability (SAT), which we adapt for the traces model of CSP. We tailor bounded model checking (BMC), that can be used for bug detection, and temporal k-induction, which aims at establishing inductiveness of properties and is capable of both bug finding and establishing the correctness of systems. Secondly, we propose a static analysis framework for establishing livelock freedom of CSP processes, with lessons for other concurrent formalisms. As opposed to traditional exhaustive state-space exploration, our framework employs a system of rules on the syntax of a process to calculate a sound approximation of its fair/co-fair sets of events. The rules either safely classify a process as livelock-free or report inconclusiveness, thereby trading accuracy for speed. Finally, we develop a series of abstraction/refinement schemes for the traces, stable-failures and failures-divergences models of CSP and embed them into a fully automated and compositional CEGAR framework. For each of those techniques we present an implementation and an experimental evaluation on a set of CSP benchmarks.
Cycloisomerization of Enynes Catalyzed by Iron(0)—Ate Complexes. (2005)

The 18-electron half-sandwich iron(0) complex [CpFe(C&lt;sub&gt;2&lt;/sub&gt;H&lt;sub&gt;4&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;] [Li(tmeda)] (&lt;b&gt;1a&lt;/b&gt;), which is readily available in multigram quantities from inexpensive starting materials (ferrocene, ethylene, Li sand), is shown to be an efficient catalyst for the Alder-ene reaction of various 1,6(7)-enynes. Thereby, the presence of the labile alkene ligands in the ferrate catalyst is essential since the analogous complex [CpFe(CO)&lt;sub&gt;2&lt;/sub&gt;]Na is catalytically incompetent. The cycloisomerizations catalyzed by &lt;b&gt;1a&lt;/b&gt; are compatible with various functional groups and turned out to be highly diastereoselective with regard to the configuration of the newly formed alkenes as well as relative stereochemistry at the ring junction. The alkyne moiety in the substrates may be terminal, silylated, or substituted with various groups, including cyclopropane rings. Likewise, the alkene substructure can be varied to a large extent, with cycloalkenes of ring sizes ≥7 being particularly suitable.
Celecoxib reduces glucocorticoids in vitro and in a mouse model with adrenocortical hyperplasia (2015)

Primary pigmented nodular adrenocortical disease (PPNAD), whether in the context of Carney complex (CNC) or isolated, leads to ACTH-independent Cushing's syndrome (CS). CNC and PPNAD are caused typically by inactivating mutations of PRKAR1A, a gene coding for the type 1a regulatory subunit (R1α) of cAMP-dependent protein kinase (PKA). Mice lacking Prkar1a, specifically in the adrenal cortex (AdKO) developed CS caused by bilateral adrenal hyperplasia (BAH), which is formed from the abnormal proliferation of fetal-like adrenocortical cells. Celecoxib is a cyclooxygenase 2 (COX2) inhibitor. In bone, Prkar1a inhibition is associated with COX2 activation and prostaglandin E2 (PGE2) production that, in turn, activates proliferation of bone stromal cells. We hypothesized that COX2 inhibition may have an effect in PPNAD. In vitro treatment of human cell lines, including one from a patient with PPNAD, with celecoxib resulted in decreased cell viability. We then treated AdKO and control mice with 1500 mg/kg celecoxib or vehicle. Celecoxib treatment led to decreased PGE2 and corticosterone levels, reduced proliferation and increased apoptosis of adrenocortical cells, and decreased steroidogenic gene expression. We conclude that, in vitro and in vivo, celecoxib led to decreased steroidogenesis. In a mouse model of PPNAD, celecoxib caused histological changes that, at least in part, reversed BAH and this was associated with a reduction of corticosterone levels.
高性能フレキシブル TFT 実現に向けたアモルファス酸化物半導体の材料探索とフレキシブル TFT 特性 (2005)

TFT 応用を見据えた材料探索指 針について説明する．また，電気特性をもとに材料探索を 行った In２O３-Ga２O３-ZnO 三元系について詳細に示す．そ して，材料探索の結果，選択したアモルファス In-Ga-Zn -O(a-IGZO)を用いた透明なフレキシブル TFT のデバ イス特性について紹介する．
Quantitative Genetics and Genomics of Adaptive Traits in Reef Building Corals (2011)

The decline of standing coral populations due to global warming is now well\ndocumented, but the prospects for the next generations of corals are not yet clear.
A guide to securing industrial control networks — (IT/OT) convergence (2017)

The following topics are dealt with: maintenance engineering; variable speed drives; electrical safety; earthing; induction motors; hazardous areas; power supply quality; IEC standards; occupational safety; electric motors.
Partial invariance for 3D layout in pictures (2010)

In pictures, outwardly directed objects (e.g., the pointing arm in the Army recruitment poster), seem to “follow” the viewer. Fronto-parallel objects (the shoulders in the poster), do not seem to follow the viewer. If objects slanted at ∼90 deg in the picture seem to follow the viewer and those at ∼0 deg do not, the perceived slant between pictured objects should change with viewing location, suggesting a failure of perceptual invariance. To investigate this, we used pictures of vertical hinges in an “open book” configuration. Observers viewed them from various azimuths and indicated the perceived angle between the sides relative to 90 deg. We varied the information for estimating picture-surface slant and geometric information in the picture background. We considered three hypotheses. 1) Retinal: Failure to take viewing location into account. 2) Perceptual-invariance: Perceiving the same 3d structure from all locations. 3) Weighted-average: Combination of slant estimates from the depicted scene and picture surface (this hypothesis is only partially consistent with invariance). With minimal picture-surface slant information (monocular viewing through aperture), the results were similar to the retinal hypothesis (no invariance). With rich surface slant information (binocular viewing, picture frame cue), they were similar to the weighted-average hypothesis (partial invariance). Varying the geometric information had no effect. The perceived layout of pictured scenes changes with viewing position, but much less so when information about the picture-surface slant is available.
Generating an Explainable ECG Beat Space With Variational Auto-Encoders (2019)

Electrocardiogram signals are omnipresent in medicine. A vital aspect in the analysis of this data is the identification and classification of heart beat types which is often done through automated algorithms. Advancements in neural networks and deep learning have led to a high classification accuracy. However, the final adoption of these models into clinical practice is limited due to the black-box nature of the methods. In this work, we explore the use of variational auto-encoders based on linear dense networks to learn human interpretable beat embeddings in time-series data. We demonstrate that using this method, an interpretable and explainable ECG beat space can be generated, set up by characteristic base beats.
Experimental Study of Engine Oil Film Thickness Dependence on Liner Location, Oil Properties and Operating Conditions (1995)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1995.
On-line diagnostics in inverter fed induction machines using high frequency signal injection (2004)

Fault diagnostics for induction machines using an injected high frequency carrier signal is presented and analyzed in this paper. Both stator winding fault and broken: rotor bar detection is covered. Measurement of the resulting high frequency negative sequence current is shown to be capable of detecting both types of faults at their incipient stage. Though sharing similar physical principles to techniques applied to line-connected machines, the use of a high frequency signal is shown to provide important advantages for inverter fed machines, such as providing the same performance and drastically reduced sensitivity to the working condition of the machine, i.e. torque and flux levels, and fundamental excitation frequency.
Differences in gut microbiota composition in metabolic syndrome and type 2 diabetes subjects in a multi-ethnic population: the HELIUS study (2020)

Abstract Recently, increased attention has been drawn to the composition of the intestinal microbiota and its possible role in metabolic syndrome and type 2 diabetes (T2DM). However, potential variation in gut microbiota composition across ethnic groups is rarely considered despite observed unequal prevalence for these diseases. Our objective was therefore to study the gut microbiota composition across health, metabolic syndrome and T2DM in a multi-ethnic population residing in the same geographical area. 16S rRNA gene sequencing was performed on fecal samples from 3926 participants to the HELIUS cohort (Amsterdam, The Netherlands), representing 6 ethnic groups (Dutch, Ghanaians, Moroccans, Turks, Surinamese of either African or South-Asian descent). Included participants completed a questionnaire and underwent a physical examination and overnight fasted blood sampling. Gut microbiota composition was compared across metabolic status (diabetes with and without metformin use, metabolic syndrome and its subsequent components, health) and ethnicities using Wilcoxon-Mann-Withney tests and logistic regressions. Overall, the gut microbiota alpha-diversity (richness, Shannon index and phylogenetic diversity) decreased with worsening of the metabolic state (comparing health to metabolic syndrome to T2DM) but this was only partially reproduced in ethnic-specific analyses. In line, a lower alpha-diversity was found in relation to all metabolic syndrome components as well as in T2DM subjects using metformin compared to non-users. Alterations, mainly decreased abundances, were also observed at the genus level (many Clostridiales) in metabolic syndrome subjects and more strongly in T2DM subjects with differences across ethnic groups. In particular, we observed decreased abundances of members of the Peptostreptococcaceae family and of Turicibacter and an increased abundance of a member of the Enterobacteriaceae family. Our data highlight several compositional differences in the gut microbiota of individuals with metabolic syndrome or T2DM. These features, confirming prior observations, give some insights into potential key intestinal bacteria related to a worsening of metabolic state. Our results also underscore possible ethnic-specific profiles associated with these microbiota alterations that should be further explored.
Feasibility Study of Economics and Performance of Solar Photovoltaics at the Former St. Marks Refinery in St. Marks, Florida (2010)

This report presents the results of an assessment of the technical and economic feasibility of deploying a photovoltaics (PV) system on a brownfield site in St. Marks, Florida. The site was assessed for possible PV installations. The cost, performance, and site impacts of different PV options were estimated. The economics of the potential systems were analyzed using an electric rate of $0.08/kWhand incentives offered in the State of Florida and from the two accessible utilities, Progress Energy and the City of Tallahassee. According to the site production calculations, the most cost-effective system in terms of return on investment is the fixed-tilt thin film technology. The report recommends financing options that could assist in the implementation of such a system.
Controlled Molecular Motions in Copper-Complexed Rotaxanes:  An XAS Study (2000)

The environment of the central metal of a molecular machine-like copper rotaxane was observed by XAS experiments. The wheel of the rotaxane is a hetero-bischelating macrocycle containing both bidentate (phenanthroline) and terdentate (terpyridine) moieties. The axle of the assembly contains only a bidentate moiety. Applying an external chemical stimulus-oxidation of the metal-increases the number of coordinating atoms required by the metal template from 4 to 5. This variation is consistent with the oscillation of the wheel around the axle, leading thus to the most stable environment for the metal in the Cu(II) rotaxane.
Sensors to Detect the Activities of Daily Living (2006)

We study the use of embedded and worn sensors to unobtrusively detect the activities of daily living (ADL). Our aim is to find the minimum set of sensors required to detect these basic tasks. In this exploratory work, we analyze the publicly available 'Intense Activity' dataset from the MIT PlaceLab project and study the classification of eating and meal preparation vs. other activities. We find that eating and meal preparation can be detected with an accuracy of 90% using less than 1/3 of the over 300 available sensors in the PlaceLab. If only 8 sensors are used, the accuracy is 82% which may be adequate for some applications.
Phase 2 Study of the Anti-Angiogenesis Agent AG-013736 in Patients with Poor Prognosis Acute Myeloid Leukemia (AML) or Myelodysplastic Syndrome (MDS). (2004)

Abstract Background: AG-013736 is a potent and selective inhibitor of VEGF, PDGF and cKit receptor tyrosine kinases with broad preclinical activity in solid tumors and an AML model. To investigate the anti-leukemic effects of AG-013736 in patients with poor prognosis AML and MDS, we performed a multicenter Phase II Trial. Methods: Eligible patients (pts) had poor prognosis AML (defined as age of pt ≥65 years, secondary AML, or unfavorable cytogenetics) or poor prognosis MDS (defined as ≥10% myeloblasts in marrow or blood). A 2-stage Simon design was employed with an “unimportant” response rate set at 10% and an “important” rate at 30%. The α and β rates were set at 0.1 with 1 response (complete or partial) in 11 pts in the first stage required before proceeding to the second stage. A successful trial required at least 5 responses in 25 pts. AG-013736 was dosed orally at 5 mg twice a day. Marrow and blood samples were taken for various markers of angiogenesis and microvessel density. Results: 12 pts (8 AML; 4 MDS) were enrolled including 1 pt who replaced a patient who was withdrawn for lack of compliance after 1 dose. Average age was 77 (range 58–88) years; 7 men, 5 women; 10 white and 2 Asian. All pts were ECOG performance status 0 (5 pts) or 1 (7). 8 pts required blood and 9 platelet transfusions. 8 pts discontinued for lack of efficacy, 3 for non-compliance, and 1 for refusal to participate further. AG-013736-related Grade 3 and 4 adverse events (AEs) included hypertension or blood pressure (BP) elevation (4), mucosal inflammation (1), and deep vein thrombosis (1). Common (&gt;10%) mild-moderate AEs included hoarseness (8 pts), diarrhea (5), BP increased or hypertension (4), proteinuria (3), and mucosal inflammation (2). 9 (75%) pts required at least 1 antihypertensive medication. There were no responses, and therefore enrollment was stopped at 12 patients. Patients received study drug for a median of 53 (range 1–190) days, and 2 pts, one with AML and one with MDS, had stable disease for 132 and 190 days, respectively. Treatment-related changes in biomarkers are being assessed. Conclusion: AG-013736 was generally well tolerated in this small cohort of elderly pts, 2 of whom had stable disease of significant duration. The combination of AG-013736 with other targeted therapies or cytotoxic agents appears feasible and may be warranted in future studies in patients with poor prognosis AML/MDS.
Characterization and modeling of clock skew with process variations (2003)

A new compact model for on-chip clock skew as a function of device, interconnect, and system parameter variations is derived. Unlike previous models that describe qualitative behavior of clock skew components, the new model provides a closed form expression for each clock skew component. An example of clock skew components for a typical design using 0.18 /spl mu/m CMOS technology is investigated.
Interleukin‐4 stimulates collagen gene expression in human fibroblast monolayer cultures Potential role in fibrosis (1992)

A role for the cytokines produced by tissue-infiltrated inflammatory cells (mainly T-lymphocytes and mast cells) in the pathophysiology of fibrosis has been suggested by several groups. Among the products of these cells, interleukin-4 (IL-4) might be one of the factors involved in the initiation of the fibrotic process. We studied the effects of recombinant human IL-4 on human fibroblast monolayer cultures. IL-4 (10 and 100 U/ml) induced a dose-dependent increase of collagen production. Non-collagen protein synthesis was not significantly altered. A concomitant increase of pro-alpha 1(I) collagen mRNAs was observed, showing that IL-4 acts at a pre-translational level.