gebhart/patrepeval huggingface dataset:
Temperature-Sensitive Alleles of <i>RSW2</i> Link the KORRIGAN Endo-1,4-β-Glucanase to Cellulose Synthesis and Cytokinesis in Arabidopsis (2001)

An 8.5-kb cosmid containing the KORRIGAN gene complements the cellulose-deficient rsw2-1 mutant of Arabidopsis. Three temperature-sensitive alleles of rsw2 show single amino acid mutations in the putative endo-1,4-beta-glucanase encoded by KOR. The F1 from crosses between kor-1 and rsw2 alleles shows a weak, temperature-sensitive root phenotype. The shoots of rsw2-1 seedlings produce less cellulose and accumulate a short chain, readily extractable glucan resembling that reported for rsw1 (which is defective in a putative glycosyltransferase required for cellulose synthesis). The double mutant (rsw2-1 rsw1) shows further reductions in cellulose production relative to both single mutants, constitutively slow root growth, and enhanced temperature-sensitive responses that are typically more severe than in either single mutant. Abnormal cytokinesis and severely reduced birefringent retardation in elongating root cell walls of rsw2 link the enzyme to cellulose production for primary cell walls and probably cell plates. The Rsw2(-) phenotype generally resembles the Kor(-) and cellulose-deficient Rsw1(-) phenotypes, but anther dehiscence is impaired in Rsw2-1(-). The findings link a second putative enzyme activity to cellulose synthesis in primary cell walls of Arabidopsis and further increases the parallels to cellulose synthesis in Agrobacterium tumefaciens where the celA and celC genes are required and encode a putative glycosyltransferase and an endo-1,4-beta-glucanase related to RSW1 and KOR, respectively.
Identifying Women With Cervical Neoplasia (1999)

For women with ASCUS Pap tests, HPV DNA testing of residual specimens collected for routine cervical cytology can help identify those who have underlying HSIL. By testing the specimen collected at initial screening, the majority of high-risk cases can be identified and referred for colposcopy based on a single screening.
Protein Delivery Using Cys <sub>2</sub> –His <sub>2</sub> Zinc-Finger Domains (2014)

The development of new methods for delivering proteins into cells is a central challenge for advancing both basic research and therapeutic applications. We previously reported that zinc-finger nuclease proteins are intrinsically cell-permeable due to the cell-penetrating activity of the Cys2-His2 zinc-finger domain. Here, we demonstrate that genetically fused zinc-finger motifs can transport proteins and enzymes into a wide range of primary and transformed mammalian cell types. We show that zinc-finger domains mediate protein uptake at efficiencies that exceed conventional protein transduction systems and do so without compromising enzyme activity. In addition, we demonstrate that zinc-finger proteins enter cells primarily through macropinocytosis and facilitate high levels of cytosolic delivery. These findings establish zinc-finger proteins as not only useful tools for targeted genome engineering but also effective reagents for protein delivery.
Continuous-wave THz imaging (2001)

The first THz imaging spectrometer based on continuous-wave THz radiation is presented. The new setup is less expensive and more compact than conventional time-domain imaging systems that comprise femtosecond lasers instead. As an example we investigate a human liver with metastasis.
Sequoia: a fault-tolerant tightly coupled multiprocessor for transaction processing (1988)

The Sequoia computer is a tightly coupled multiprocessor that avoids most of the fault-tolerance disadvantages of tight coupling by using a fault-tolerant hardware-design approach. An overview is give of how the hardware architecture and operating system (OS) work together to provide a high degree of fault tolerance with good system performance. A description of hardware is followed by a discussion of the multiprocessor synchronization problem. Kernel support for fault recovery and the recovery process itself are examined. It is shown the kernel, through a combination of locking, shadowed memory, and controlled flushing of non-write-through cache, maintains a consistent main memory state recoverable from any single-point failure. The user shared memory is also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Cyclins and Cyclin Dependent Kinases during Cardiac Development (1997)

The molecular mechanisms that regulate the cardiomyocyte cell cycle and its terminal differentiation remain largely unknown. To determine which cyclins or cyclin dependent kinases (CDKs) are important for cardiomyocyte proliferation, we examined the expression of cyclins and CDKs during normal cardiac development. All cyclins and CDKs were highly expressed during embryonic cardiac development, then they decreased at different rates after birth. The mRNAs and proteins of cyclins A and B (G2 and M phase cyclins) were found in embryonic and neonatal hearts, but were not detected in young or adult hearts. In contrast, while the mRNAs of cyclins D1, D2, D3, and E (G1 and S phase cyclins) were observed during all stages of development, the proteins of cyclins D1, D3, and E were observed in hearts at the young growth stage, although the levels decreased differently. Reverse transcriptase-polymerase chain reaction (RT-PCR) using specific cyclin B and D3 primers revealed that cyclins B and D3 originated from cardiomyocytes and noncardiomyocytes. The CDKs (cdc2, CDK2, and CDK4) were highly expressed during embryonic cardiac development and maintained almost constant levels during neonatal periods. However, they were expressed at very low levels at the young and adult stages. The pattern of proliferating cell nuclear antigen (PCNA) expression during cardiac development was similar to the expression of CDKs. These findings suggest that all cyclins and CDKs are involved in the cardiac cell cycle, and that marked and rapid reduction of mitotic cyclins may be associated with the withdrawal of the cardiac cell cycle after birth.
Ethnobotanik und Pharmaziegeschichte - gemeinsame Herausforderungen und Aufgaben (2005)

In this paper we use two disparate examples to highlight the relevance of historical methods in the context of ethnobotany and ethnopharmacy. The history of pharmacy - as it relates to phytotherapy and medicinal plants - has had a strong interest in what anthropologists would call ‘cultural practises'. The antiquity of medicinal plant uses in the Olmec region in Mexico was studied by comparing the pharmacopoeias of the linguistically related Lowland Mixe and Zoque-Popoluca. These cultures, separated for about 2000 years, have cognates for vernacular medicinal plant names in common. For fifteen species such cognate names were detected. Also, a statistically significant segment of the medicinal flora is used for similar purposes. Overall, 123 species are shared between the two groups and 62 of these have a similar usage. These findings make a transmission of such knowledge since the time of the Olmecs highly likely.\nThe Ch'orti' of Eastern Guatemala provide another interesting example of the relevance of historical data. Cultural anthropologist Charles Wisdom compiled an unpublished MS with many tentatively identified medicinal plant species used in the region in the 1930s - a rare chance for an ethnopharmacist.\nOverall, these data indicate that we need to ascertain that such information is publicly available in order to safeguard the original keepers of knowledge and their rights.
On the effective prevention of TLS man-in-the-middle attacks in web applications (2014)

In this paper we consider TLS Man-In-The-Middle (MITM) attacks in the context of web applications, where the attacker is able to successfully impersonate the legitimate server to the user, with the goal of impersonating the user to the server and thus compromising the user&apos;s online account and data. We describe in detail why the recently proposed client authentication protocols based on TLS Channel IDs, as well as client web authentication in general, cannot fully prevent such attacks.\n\nNevertheless, we show that strong client authentication, such as Channel ID-based authentication, can be combined with the concept of server invariance, a weaker and easier to achieve property than server authentication, in order to protect against the considered attacks. We specifically leverage Channel ID-based authentication in combination with server invariance to create a novel mechanism that we call SISCA: Server Invariance with Strong Client Authentication. SISCA resists user impersonation via TLS MITM attacks, regardless of how the attacker is able to successfully achieve server impersonation. We analyze our proposal and show how it can be integrated in today&apos;s web infrastructure.
Effect of seasoning-layer stress on fluorine diffusion (2020)

In semiconductor thin-film deposition equipment in which a fluorine- or chlorine-based gas is used as a cleaning gas, reducing residual fluorine or chlorine inside the equipment is important for increasing production efficiency and reducing production costs. In the plasma-enhanced chemical vapor deposition process, where cleaning, seasoning, and deposition are sequentially repeated, an AlF3 layer is formed during the cleaning step with fluorine; the physical properties of the seasoning layer in contact with the AlF3 layer play an important role in fluorine diffusion. When the seasoning layer exhibits high compressive stress, the adsorbed fluorine does not diffuse and accelerates damage as it continuously concentrates on the surface of the aluminum component. We demonstrate the relationship between stress in the seasoning layer and fluorine diffusion and show that relieving compressive stress promotes fluorine diffusion, which, in turn, reduces the amount of fluorine inside aluminum components.
Artificial Cells for Bioencapsulation of Cells and Genetically Engineered E. coli: For Cell Therapy, Gene Therapy, and Removal of Urea and Ammonia (2003)

Enzymes, proteins, cells, microorganisms, adsorbents, magnetic materials and other biologically active materials can be encapsulated within artificial cells with artificial polymer membranes (1–9). This type of artificial cells are not liposomes. The artificial cells protect the encapsulated biological materials from immunological reactions. At the same time, the enclosed materials continue to act in the immunologically isolated environment. The use of artificial cells containing adsorbent for hemoperfusion is a routine procedure used in patients for the removal of toxic substances or unwanted metabolites. Clinical studies are ongoing in patients using artificial cells as red blood cell substitutes, for enzyme therapy, and for delivery of biotechnological agents. Chang first developed a drop method for the bioencapsulation of cells and proposed its use in cell therapy (4,5). “Micro encapsulation of intact cells … the enclosed material might be protected from destruction and from participation in immunological processes, whereas the enclosing membrane would be permeable to small molecules of specific cellular product which could then enter the general extracellular compartment of the recipient. … The situation is comparable to that of a graft placed in an immunologically favorable site” (4). This was not explored by others for sometime. However, with increasing interests in biotechnology, many groups are now actively studying this for bioencapsulation of cells or genetically engineered microorganisms in cell and gene therapy. This chapter describes only two examples: bioencapsulation of hepatocytes or genetically engineered microorganisms. These examples are used to demonstrate the methods of preparations and their potential applications in cell and gene therapy.
Dietary fiber prevents obesity-related liver lipotoxicity by modulating sterol-regulatory element binding protein pathway in C57BL/6J mice fed a high-fat/cholesterol diet (2015)

Adequate intake of dietary fibers has proven metabolic and cardiovascular benefits, molecular mechanisms remain still limited. This study was aimed to investigate the effects of cereal dietary fiber on obesity-related liver lipotoxicity in C57BL/6J mice fed a high-fat/cholesterol (HFC) diet and underlying mechanism. Forty-eight adult male C57BL/6J mice were randomly given a reference chow diet, or a high fat/cholesterol (HFC) diet supplemented with or without oat fiber or wheat bran fiber for 24 weeks. Our results showed mice fed oat or wheat bran fiber exhibited lower weight gain, lipid profiles and insulin resistance, compared with HFC diet. The two cereal dietary fibers potently decreased protein expressions of sterol regulatory element binding protein-1 and key factors involved in lipogenesis, including fatty acid synthase and acetyl-CoA carboxylase in target tissues. At molecular level, the two cereal dietary fibers augmented protein expressions of peroxisome proliferator-activated receptor alpha and gamma, liver X receptor alpha, and ATP-binding cassette transporter A1 in target tissues. Our findings indicated that cereal dietary fiber supplementation abrogated obesity-related liver lipotoxicity and dyslipidemia in C57BL/6J mice fed a HFC diet. In addition, the efficacy of oat fiber is greater than wheat bran fiber in normalizing these metabolic disorders and pathological profiles.
Dyslipidemia in Patients with Nonalcoholic Fatty Liver Disease (2012)

Patients with nonalcoholic fatty liver disease (NAFLD) often have dyslipidemia along with other features of metabolic syndrome such as obesity, diabetes mellitus, and hypertension. The dyslipidemia in NAFLD is characterized by increased serum triglycerides, increased small, dense low-density lipoprotein (LDL nontype A) particles, and low high-density lipoprotein (HDL) cholesterol. The pathogenesis of dyslipidemia in NAFLD is not well understood, but it is likely related to hepatic overproduction of the very low-density lipoprotein particles and dysregulated clearance of lipoproteins from the circulation. There is unequivocal evidence that cardiovascular disease is the most common cause of mortality in patients with NAFLD. Aggressive treatment of dyslipidemia plays a critical role in the overall management of patients with NAFLD. Statins are the first-line agents to treat high cholesterol and their dosage should be adjusted based on achieving therapeutic targets and tolerability. Although all statins appear to be effective in improving cholesterol levels in patients with NAFLD, there is more experience with atorvastatin in patients with NAFLD; furthermore, it is the only statin to date to show a reduced cardiovascular morbidity in patients with NAFLD. The risk for serious liver injury from statins is quite rare and patients with NAFLD are not at increased risk for statin hepatotoxicity. Omega-3 fatty acids are perhaps the first choice to treat hypertriglyceridemia because of their safety, tolerability, and efficacy in improving serum triglycerides, as well as their potential to improve liver disease.
12-ps ECL using low-base-resistance Si bipolar transistor by self-aligned metal/IDP technology (1997)

A self-aligned metal/IDP (SMI) technology is proposed to reduce the external base resistance and to enable fabrication of high-speed bipolar transistors. This SMI technology produces a self-aligned base electrode of stacked layers of metal and in situ-doped poly-Si (LDP) with a small thermal budget by selective tungsten CVD. It provides the low base resistance and a shallow link base for the small-collector capacitance and the high-cutoff frequency. The base resistance is reduced to a half that in a transistor having a conventional poly-Si base electrode. A maximum oscillation frequency of 81 GHz and a 12.2-ps gate delay time in an ECL ring oscillator at a voltage swing of 250 mV were achieved by using the SMI technology even with an ion-implanted base.
Facial expression recognition with temporal modeling of shapes (2011)

Conditional Random Fields (CRFs) can be used as a discriminative approach for simultaneous sequence segmentation and frame labeling. Latent-Dynamic Conditional Random Fields (LDCRFs) incorporates hidden state variables within CRFs which model sub-structure motion patterns and dynamics between labels. Motivated by the success of LDCRFs in gesture recognition, we propose a framework for automatic facial expression recognition from continuous video sequence by modeling temporal variations within shapes using LDCRFs. We show that the proposed approach outperforms CRFs for recognizing facial expressions. Using Principal Component Analysis (PCA) we study the separability of various expression classes in lower dimension projected spaces. By comparing the performance of CRFs and LDCRFs against that of Support Vector Machines (SVMs), we demonstrate that temporal variations within shapes are crucial in classifying expressions especially for those with a small range of facial motion like anger and sadness. We also show empirically that only using changes in facial appearance over time, without using shape variations, is not sufficient to obtain high performance for facial expression recognition.
Feasibility of Eliminating the Use of Highly Enriched Uranium in the Production of Medical Radioisotopes (2006)

Significant quantities of highly enriched uranium (HEU)—more than enough to make a Hiroshima bomb—are used annually as neutron target material in Canadian, European, and South African reactors to produce the short-lived fission products used in nuclear medicine. The most important of these fission products is 99Mo, which decays into 99mTc, which is the most widely used medical radioisotope. The U.S. supplies weapon-grade uranium to the Canadian radioisotope producer and might in the future provide it to the European producers as well. As a condition for receiving U.S. HEU, the 1992 Schumer Amendment to the U.S. Atomic Energy Act requires that a foreign producer cooperate with the United States in converting to low-enriched uranium (LEU) targets. Some smaller producers have already done so. The Canadian producer has asserted, however, that the cost of conversion would be too high. The 2005 Burr amendment therefore exempted radioisotope producers in Canada and Europe from the Schumer amendment's requirements but requested a National Academy of Sciences study of the feasibility of conversion, setting as a feasibility test that the production cost be increased by no more than 10 percent. We show that paying for the conversion for the largest European production facility would increase the cost of 99Mo production there by only a few percent. For the Canadian facility the production cost could be more than 10 percent but the increase in the cost of the final 99mTc-containing radiopharmaceutical would be only about 1 percent. It is also pointed out that savings in security could well dwarf the costs of converting to LEU if HEU were no longer present at the production and radioactive waste sites.
Stacking effects on dielectric properties of sol-gel derived Pb(Zr0.53Ti0.47)O3/PbTiO3 thin films (1998)

A thin film multilayer structure consisting of Pb(Zr0.53Ti0.47)O3(PZT) and PbTiO3(PT) were fabricated by a sol-gel process. The effects of the number of PZT/PT layers upon microstructure and dielectric characteristics were investigated. For a pure PZT thin layer annealed at 600 °C, the microstructure observed was a rosette type, whereas the insertion of PT interlayers yielded thin films with homogeneous grain distribution regardless of the number of PZT/PT layers. With increasing number of PZT/PT layers, the leakage current density and coercive field effectively decreased, while the dielectric constant increased. Loss tangent and fixed charge were found to be independent of the number of PZT/PT layers. These results are possibly explained by the enhanced crystallization resulting from the introduction of large number of nucleation sites in the multilayer film, and by the stacking of stable and dense PZT/PT layers. The thin film composed of three PZT/PT layers with a thickness of ∼450 nm exhibited dielectric constant of 1000, remnant polarization of 20 μC/cm2, coercive field of 40 kV/cm, and tan δ of 0.03. The relaxorlike ferroelectric behavior was observed with an increasing number of PZT/PT layers.
Adaptive ordering of pipelined stream filters (2004)

We consider the problem of pipelined filters, where a continuous stream of tuples is processed by a set of commutative filters. Pipelined filters are common in stream applications and capture a large class of multiway stream joins. We focus on the problem of ordering the filters adaptively to minimize processing cost in an environment where stream and filter characteristics vary unpredictably over time. Our core algorithm, A-Greedy (for Adaptive Greedy), has strong theoretical guarantees: If stream and filter characteristics were to stabilize, A-Greedy would converge to an ordering within a small constant factor of optimal. (In experiments A-Greedy usually converges to the optimal ordering.) One very important feature of A-Greedy is that it monitors and responds to selectivities that are correlated across filters (i.e., that are nonindependent), which provides the strong quality guarantee but incurs run-time overhead. We identify a three-way tradeoff among provable convergence to good orderings, run-time overhead, and speed of adaptivity. We develop a suite of variants of A-Greedy that lie at different points on this tradeoff spectrum. We have implemented all our algorithms in the STREAM prototype Data Stream Management System and a thorough performance evaluation is presented.
Elastic IP and security groups implementation using OpenFlow (2012)

This paper presents a reference implementation of an Elastic IP and Security Group service using the OpenFlow protocol. The implementation is the first to present integration of OpenFlow within a virtual machine provisioning engine and an API for enabling such services. In this paper the OpenNebula system is used. The Elastic IP and Security Groups services are similar to the Amazon EC2 services and present a compatible Query API implemented by OpenNebula. The core of the implementation relies on the integration of an OpenFlow controller (NOX) with the EC2 server. Flow rules can be inserted in the OpenFlow controller using the EC2 API. These rules are then used by Open vSwitch bridges on the underlying hypervisor to manage network traffic. The reference implementation presented opens the door for more advanced cloud networking services that leverage principles from software defined networking including virtual private cloud, virtual data center spanning multiple availability zones, as well as seamless migration over wide are networks.