gebhart/patrepeval huggingface dataset:
Acanthamoeba keratitis in England and Wales: incidence, outcome, and risk factors (2002)

The incidence was considerably higher than most previous estimates, and was static. The geographical variation in incidence may be partly related to the increase in risk associated with hard water. The fact that water quality can have such an effect on the risk of AK suggests that many CL wearers must be letting tapwater come into contact with their lenses or storage cases. Improved education for CL wearers and practitioners about hygiene practice and the variable efficacy of contact lens systems could be expected to reduce the incidence of this disease.
Phenotypic analysis of conditionally immortalized cells isolated from the BPK model of ARPKD (2001)

To study the pathophysiology of autosomal recessive polycystic kidney disease (ARPKD), we sought to develop conditionally immortalized control and cystic murine collecting tubule (CT) cell lines. CT cells were isolated from intercross breedings between BPK mice (bpk(+/-)), a murine model of ARPKD, and the Immorto mice (H-2K(b)-ts-A58(+/+)). Second-generation outbred offspring (BPK x Immorto) homozygous for the BPK mutation (bpk(-/-); Im(+/+/-); cystic BPK/H-2K(b)-ts-A58), were phenotypically indistinguishable from inbred cystic BPK animals (bpk(-/-)). Cystic BPK/H-2K(b)-ts-A58 mice developed biliary ductal ectasia and massively enlarged kidneys, leading to renal failure and death by postnatal day 24. Principal cells (PC) were isolated from outbred cystic and noncystic BPK/H-2K(b)-ts-A58 littermates at specific developmental stages. Epithelial monolayers were under nonpermissive conditions for markers of epithelial cell polarity and PC function. Cystic and noncystic cells displayed several properties characteristic of PCs in vivo, including amiloride-sensitive sodium transport and aquaporin 2 expression. Cystic cells exhibited apical epidermal growth factor receptor (EGFR) mislocalization but normal expression of ZO-1 and E-cadherin. Hence, these cell lines retain the requisite characteristics of PCs, and cystic BPK/H-2K(b)-ts-A58 PCs retained the abnormal EGFR membrane expression characteristic of ARPKD. These cell lines represent important new reagents for studying the pathogenesis of ARPKD.
Identification of Differentially Expressed Genes through Integrated Study of Alzheimer’s Disease Affected Brain Regions (2016)

We find genes related with AD that are consistent with existing studies, and new candidate genes not previously related with AD. Our study confirms the up-regualtion of INFAR2 and PTMA along with the down regulation of GPHN, RAB2A, PSMD14 and FGF. Novel genes PSMB2, WNK1, RPL15, SEMA4C, RWDD2A and LARGE are found to be differentially expressed across all brain regions. Further investigation on these genes may provide new insights into the development of AD. In addition, we identified the presence of 23 non-coding features, including four miRNA precursors (miR-7, miR570, miR-1229 and miR-6821), dysregulated across the brain regions. Furthermore, we compared our results with two popular meta-analysis methods RankProd and GeneMeta to validate our findings and performed a sensitivity analysis by removing one dataset at a time to assess the robustness of our results. These new findings may provide new insights into the disease mechanisms and thus make a significant contribution in the near future towards understanding, prevention and cure of AD.
Regulation and Kinetics of the Actin-Myosin-ATP Interaction (1980)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Phase Transitions and Switching Behavior in a Fluorine-Containing Ferroelectric Liquid Crystal (1989)

Phase transitions and switching behavior in a fluorine containing ferroelectric liquid crystal, whose optical purity was controlled by mixing (R) and (S) enantiomorphs, were studied. Only for the pure (R) or (S) enantiomorphs, the phase transition from the SmA to the third state SmC A * , occurred directly. For the mixtures of (R) and (S) enantiomorphs, the phase transition occurred from the SmA to the SmC A * via the SmC * . In these mixtures, with decreasing temperature in SmC * , internal disclination loops changed from “boat type” to “stripe type”.
Neurobiologic Processes in Drug Reward and Addiction (2004)

Neurophysiologic processes underlie the uncontrolled, compulsive behaviors defining the addicted state. These"hard-wired"changes in the brain are considered critical for the transition from casual to addictive drug use. This review of preclinical and clinical (primarily neuroimaging) studies will describe how the delineation between pleasure, reward, and addiction has evolved as our understanding of the biologic mechanisms underlying these processes has progressed. Although the mesolimbic dopaminergic efflux associated with drug reward was previously considered the biologic equivalent of pleasure, dopaminergic activation occurs in the presence of unexpected and novel stimuli (either pleasurable or aversive) and appears to determine the motivational state of wanting or expectation. The persistent release of dopamine during chronic drug use progressively recruits limbic brain regions and the prefrontal cortex, embedding drug cues into the amygdala (through glutaminergic mechanisms) and involving the amygdala, anterior cingulate, orbitofrontal cortex, and dorsolateral prefrontal cortex in the obsessive craving for drugs. The abstinent, addicted brain is subsequently primed to return to drug use when triggered by a single use of drug, contextual drug cues, craving, or stress, with each process defined by a relatively distinct brain region or neural pathway. The compulsive drive toward drug use is complemented by deficits in impulse control and decision making, which are also mediated by the orbitofrontal cortex and anterior cingulate. Within this framework, future targets for pharmacologic treatment are suggested.
Using Mobile Phones to Monitor Shopping Time at Physical Stores (2011)

This article discusses the usage of mobile phones to monitor shopping time at physical stores. A phone-based shopping tracker transforms the problem of monitoring shopping time into a classification problem. It uses motif groups to identify movement trajectories based on spatial and temporal features embedded in each motif.
Enhanced Visible-Light Activity of Titania via Confinement inside Carbon Nanotubes (2011)

Titania confined inside carbon nanotubes (CNTs) was synthesized using a restrained hydrolysis method. Raman spectra and magnetic measurements using a SQUID magnetometer suggested the formation of remarkable oxygen vacancies over the encapsulated TiO(2) in comparison with nanoparticles dispersed on the outer surface of CNTs, extending the photoresponse of TiO(2) from the UV to the visible-light region. The CNT-confined TiO(2) exhibited improved visible-light activity in the degradation of methylene blue (MB) relative to the outside titania and commercial P25, which is attributed to the modification of the electronic structure of TiO(2) induced by the unique confinement inside CNTs. These results provide further insight into the effect of confinement within CNTs, and the composites are expected to be promising for applications in visible-light photocatalysis.
The growth of brain tumors can be suppressed by multiple transplantation of mesenchymal stem cells expressing cytosine deaminase (2010)

Suicide genes have recently emerged as an attractive alternative therapy for the treatment of various types of intractable cancers. The efficacy of suicide gene therapy relies on efficient gene delivery to target tissues and the localized concentration of final gene products. Here, we showed a potential ex vivo therapy that used mesenchymal stem cells (MSCs) as cellular vehicles to deliver a bacterial suicide gene, cytosine deaminase (CD) to brain tumors. MSCs were engineered to produce CD enzymes at various levels using different promoters. When co-cultured, CD-expressing MSCs had a bystander, anti-cancer effect on neighboring C6 glioma cells in proportion to the levels of CD enzymes that could convert a nontoxic prodrug, 5-fluorocytosine (5-FC) into cytotoxic 5-fluorouracil (5-FU) in vitro. Consistent with the in vitro results, for early stage brain tumors induced by intracranial inoculation of C6 cells, transplantation of CD-expressing MSCs reduced tumor mass in proportion to 5-FC dosages. However, for later stage, established tumors, a single treatment was insufficient, but only multiple transplantations were able to successfully repress tumor growth. Our findings indicate that the level of total CD enzyme activity is a critical parameter that is likely to affect the clinical efficacy for CD gene therapy. Our results also highlight the potential advantages of autograftable MSCs compared with other types of allogeneic stem cells for the treatment of recurrent glioblastomas through repetitive treatments.
Wound Teleconsultation in Patients with Chronic Leg Ulcers (2005)

Our results suggest that teledermatology offers great potential for the future in chronic wound care. By reducing the need to travel long distances to the hospital or to consult a physician with expertise in wound care, wound teleconsultation might lower health care costs and improve the quality of life for patients with chronic wounds, while still maintaining a high quality of wound care.
Secure modular password authentication for the web using channel bindings (2016)

Secure protocols for password-based user authentication are well-studied in the cryptographic literature but have failed to see wide-spread adoption on the internet; most proposals to date require extensive modifications to the Transport Layer Security (TLS) protocol, making deployment challenging. Recently, a few modular designs have been proposed in which a cryptographically secure password-based mutual authentication protocol is run inside a confidential (but not necessarily authenticated) channel such as TLS; the password protocol is bound to the established channel to prevent active attacks. Such protocols are useful in practice for a variety of reasons: security no longer relies on users’ ability to validate server certificates and can potentially be implemented with no modifications to the secure channel protocol library. We provide a systematic study of such authentication protocols. Building on recent advances in modeling TLS, we give a formal definition of the intended security goal, which we call password-authenticated and confidential channel establishment (PACCE). We show generically that combining a secure channel protocol, such as TLS, with a password authentication or password-authenticated key exchange protocol, where the two protocols are bound together using the transcript of the secure channel’s handshake, the server’s certificate, or the server’s domain name, results in a secure PACCE protocol. Our prototypes based on TLS are available as a cross-platform client-side Firefox browser extension as well as an Android application and a server-side web application that can easily be installed on servers.
Entry of the toxic proteins abrin, modeccin, ricin, and diphtheria toxin into cells. II. Effect of pH, metabolic inhibitors, and ionophores and evidence for toxin penetration from endocytotic vesicles. (1982)

The toxicity of abrin, modeccin, and ricin to Vero cells was maximal at neutral and slightly alkaline pH, and it was strongly reduced at pH 6.0 and below. Diphtheria toxin was most toxic at low pH. Binding and endocytosis of abrin, modeccin, and ricin did not vary much within the pH range tested. High concentrations of the carboxylic ionophore Br-X-537A, protected against all four toxins. Combined treatment of cells with an inhibitor of glycolysis and an uncoupler of oxidative phosphorylation strongly inhibited endocytosis of toxins and protected against intoxication. The protective effect of Ca2+ deprivation, of pH 6.0, and of metabolic inhibitors disappeared soon after transfer of the cells to normal medium, whereas the protective effect of Br-X-537A and of trifluoperazine disappeared slowly. The decay rate of the protection by NH4Cl and by the ionophore A23187 differed with the different toxins. Cells exposed to abrin, modeccin, and ricin under protective conditions which did not inhibit endocytosis of the toxins (Ca2+ deprivation, pH 6.0, Br-X-537A), and then treated with antitoxins to inactivate extracellular toxin, were intoxicated when the protection was released. In contrast, cells exposed to toxins while endocytosis was arrested by treatment with metabolic inhibitors were not intoxicated when antitoxins were added and the metabolic inhibitors removed. Modeccin and diphtheria toxin endocytosed in the presence of trifluoperazine and NH4Cl were unable to intoxicate cells. The possibility that endocytosis is a step in the normal entry route of the toxins is discussed.
Alteration of nuclear architecture in male germ cells of chromosomally derived subfertile mice (2001)

The mammalian cell nucleus consists of numerous compartments involved in the regular unfolding of processes such as DNA replication and transcription, RNA maturation, protein synthesis and cell division. Knowledge is increasing of the relationships between high-order levels of chromatin organization and its spatial organization, and of how these relationships contribute to the various functions carried out in the nucleus. We have studied the spatial arrangement of mouse telocentric chromosomes 5, 11, 13, 15, 16 and 17, some of their metacentric Robertsonian derivatives, and X and Y chromosomes by whole chromosome painting in male germ (spermatogonia, pachytene spermatocytes and spermatids) and Sertoli cells of homozygous and heterozygous individuals. Using dual-colour fluorescence in situ hybridization we found that these chromosomes occupy specific nuclear territories in each cell type analysed. When chromosomes are present as Robertsonian metacentrics in the heterozygous state, that is, as Robertsonian metacentrics and their homologous telocentrics, differences in their nuclear positions are detectable: heterozygosity regularly produces a change in the nuclear position of one of the two homologous telocentrics in all the cell types studied. In the Robertsonian heterozygotes, the vast majority of the Sertoli cells show the sex chromosomes in a condensed state, whereas they appear decondensed in the Robertsonian homozygotes. As the Robertsonian heterozygosities we studied produce a chromosomally derived impairment of male germ-cell differentiation, we discuss the possibility that changes in chromosome spatial territories may alter some nuclear machinery (e.g., synapsis, differential gene expression) important for the correct unfolding of the meiotic process and for the proper functioning of Sertoli cells.
Cats with Genetic Variants of AGXT2 Respond Differently to a Dietary Intervention Known to Reduce the Risk of Calcium Oxalate Stone Formation (2022)

This study was completed to evaluate a genotype-specific nutritional intervention for reducing the risk of calcium oxalate stone formation. Serum metabolomic profiles and genotypes of 445 cats in the colony at Hill’s Pet Nutrition, Inc (Topeka, KS, USA)were assessed in a genome-wide association study, and revealed an association between genetic variants of alanine-glyoxylate aminotransferase 2 (AGXT2) and 2-oxoarginine. The most significant single nucleotide polymorphisms (SNP) associated with 2-oxoarginine was at position chrA1:212069607, [G/A] (p < 3.687 × 10−17). This SNP explained approximately 15% of the variance in 2-oxoarginine concentrations. The distribution of genotype frequencies was 0.07 AA, 0.39 AG, and 0.54 GG, with a mean relative 2-oxoarginine concentration for each genotype of 0.45 AA, 0.92 AG, and 1.27 GG, indicating a subtractive effect of the minor allele (A). Serum concentrations of two AGXT2 substrates, symmetric/asymmetric dimethylarginines (SDMA/ADMA) and β-aminoisobutyrate (BAIB) were also strongly associated with SNP chrA1:212069607 (p < 1.43 × 10−12 and p < 2.30 × 10−14, respectively). These two AGXT2 substrates were increased with the minor allele (A), indicating that the variant of the AGXT2 gene results in decreased aminotransferase activity. Additionally, the lifetime history of stone incidence showed that cats with the AA variant of AGXT2 SNP had a 2.515× increased incidence of stones compared with cats having the GG variant (p = 0.019). In a subsequent study assessing AGXT2 genotypes, cats (n = 10 GG, 4 AG, 9 AA) were fed control or test food (containing betaine at 0.500%, and the botanicals green tea, fenugreek and tulsi at 0.25, 0.025, and 0.0015%, respectively) in a cross-over study design. Stone risk analysis was conducted on urine samples after feeding control or test food for 28 days each. A calcium oxalate titration test (COT) was performed to assess the amount of added Ox−2 (per L) required to initiate calcium oxalate crystal formation. Cats with the GG variant of the AGXT2 SNP required more added oxalate to initiate urine crystal formation after consuming test food compared with control food, indicating a decreased risk of oxalate crystal formation in GG cats. In addition, urine oxalate concentrations showed an overall effect of test food independent of genotype (p = 0.0009), which resulted in lower oxalate concentrations after consuming test food compared with control food. These data indicate that cats with the GG-specific variant of AGXT2 should benefit from a reduced risk of calcium oxalate stone formation after consuming a betaine and botanical dietary enhancement.
Beneficial Endocrine but Adverse Exocrine Effects of Sitagliptin in the Human Islet Amyloid Polypeptide Transgenic Rat Model of Type 2 Diabetes (2009)

OBJECTIVE We sought to establish the extent and mechanisms by which sitagliptin and metformin singly and in combination modify islet disease progression in human islet amyloid polypeptide transgenic (HIP) rats, a model for type 2 diabetes. RESEARCH DESIGN AND METHODS HIP rats were treated with sitagliptin, metformin, sitagliptin plus metformin, or no drug as controls for 12 weeks. Fasting blood glucose, insulin sensitivity, and β-cell mass, function, and turnover were measured in each group. RESULTS Sitagliptin plus metformin had synergistic effects to preserve β-cell mass in HIP rats. Metformin more than sitagliptin inhibited β-cell apoptosis. Metformin enhanced hepatic insulin sensitivity; sitagliptin enhanced extrahepatic insulin sensitivity with a synergistic effect in combination. β-Cell function was partially preserved by sitagliptin plus metformin. However, sitagliptin treatment was associated with increased pancreatic ductal turnover, ductal metaplasia, and, in one rat, pancreatitis. CONCLUSIONS The combination of metformin and sitagliptin had synergistic actions to preserve β-cell mass and function and enhance insulin sensitivity in the HIP rat model of type 2 diabetes. However, adverse actions of sitagliptin treatment on exocrine pancreas raise concerns that require further evaluation.
Media composition for casual users (2003)

An application, called Movie-Recorder has interface elements which are designed to simplify two core activities of media composition: the capture of digital movies from analog devices and, the control and editing of the captured movies. MovieRecorder has been developed for digitizing Quicktime movies from 'live' or 'uncontrolled' sources, i.e. VCRs or cameras whose video frames cannot be accurately addressed by the computer. The focus is on live capture since such devices are now more widespread than controllable laserdiscs or frame-accurate VCRs. MovieRecorder is designed primarily for non-expert or casual users. Hence, the design goal was to keep the interface as simple as possible while providing motivated users adequate control over the recording process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Path Generation Using ${\mbi \eta}^4$-Splines for a Truck and Trailer Vehicle (2013)

Generation of high-quality drive paths is a significant issue for automated wheeled vehicles. To achieve this aim for a truck and trailer vehicle, the paper proposes the use of a parameterized curve primitive, the <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">${\mbi \eta}^4$</tex></formula> -spline. Using this spline, generation and shaping of smooth feasible paths is made possible as well as the transfer between arbitrary dynamic configurations of the articulated vehicle. The <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\mbi \eta}^4$</tex> </formula> -spline is a ninth-order polynomial curve that can interpolate given Cartesian points with associated arbitrary unit tangent vector, curvature, and first and second derivatives of curvature. It depends on a set of eight (eta) parameters that can be freely chosen to modify the path shape without changing the interpolations conditions at the path endpoints. Completeness, minimality, and symmetry of the <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\mbi \eta}^4$</tex></formula> -spline are established. An example on a parking maneuver of the articulated vehicle is presented and the pertinent optimal path planning is also discussed.
Stochastic trajectory modeling for speech recognition (2002)

Models observations of phoneme-based speech units as clusters of trajectories in their parameter space. The trajectories are modeled by a mixture of state sequences of multi-variate Gaussian density functions, optimized at the state sequence level. The duration of trajectories are integrated in the modeling. The authors also provide an algorithm for sentence recognition based on the modeling. In an alphabet recognition task the resulting system trained in context-independent mode demonstrated substantially better recognition accuracy, compared to a conventional context-dependent, whole word HMM.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Molecular Dynamics Simulations on Gate Opening in ZIF-8: Identification of Factors for Ethane and Propane Separation (2013)

Gate opening of zeolitic imidazolate frameworks (ZIFs) is an important microscopic phenomenon in explaining the adsorption, diffusion, and separation processes for large guest molecules. We present a force field, with input from density functional theory (DFT) calculations, for the molecular dynamics simulation on the gate opening in ZIF-8. The computed self-diffusivities for sorbed C1 to C3 hydrocarbons were in good agreement with the experimental values. The observed sharp diffusion separation from C2H6 to C3H8 was elucidated by investigating the conformations of the guest molecules integrated with the flexibility of the host framework.
Establishment of IL-5-Dependent Early B Cell Lines by Long-Term Bone Marrow Cultures (1989)

We established two different IL-5-dependent Ly1+ early B cell lines in long-term bone marrow culture system. One of them (J-87) is stromal cell (ST2) dependent and the other (T-88) is ST2 independent. Both J-87 and T-88 are B220+, Ly1+, sIgM-, Ia-, Thy1-, and IL-2R+, and respond to IL-3 and IL-5 in the presence of ST2. The T-88 can proliferate only in response to IL-5 in the absence of ST2. Southern blot analysis using JH probe revealed that configuration of IgH gene of both cell lines shows rearranged pattern. Binding assay for radiolabeled IL-5 to T-88 demonstrated that T-88 has two classes of IL-5 binding sites (low and high affinity) on the membrane. These data strongly suggest that there are IL-5-sensitive stages at both stromal cell-dependent and stromal cell-independent phases in early B cell development.