gebhart/patrepeval huggingface dataset:
Molecular cloning of a gene involved in lipooligosaccharide biosynthesis and virulence expression by <i>Haemophilus influenzae</i> type B (1991)

A wild-type Haemophilus influenzae type b (Hib) genomic DNA library was constructed in the plasmid shuttle vector pGJB103. A virulence-deficient lipooligosaccharide (LOS) mutant of Hib was used as a recipient for genetic transformation to screen this Hib genomic DNA library for genes involved in LOS expression. A recombinant plasmid containing a 7.8 kb PstI fragment of Hib DNA was shown to transform this LOS mutant to reactivity with a monoclonal antibody (mAb) specific for a wild-type LOS epitope. Transformation of two different virulence-deficient LOS mutants with a 4.4 kb BglII fragment of this recombinant plasmid yielded transformants which expressed LOS that bound the wild-type LOS-specific mAb and yielded profiles in sodium dodecyl sulphate/polyacrylamide gradient gel electrophoresis different from those of the original LOS mutants. These transformants with structurally altered LOS molecules also exhibited increased virulence in an animal model for invasive Hib disease. The virulence-transforming ability was further localized to a 1.8 kb BglII-AlwNI fragment of the Hib DNA insert. Nucleotide sequence analysis indicated the presence of a single large open reading frame within this fragment. This open reading frame contained 19 consecutive repeats of the tetramer CAAT near the 5' end. Linker insertion mutagenesis was used to demonstrate directly the involvement of this open reading frame in both LOS biosynthesis and virulence expression by Hib.
Sparse Feature Extraction for Pose-Tolerant Face Recognition (2014)

Automatic face recognition performance has been steadily improving over years of research, however it remains significantly affected by a number of factors such as illumination, pose, expression, resolution and other factors that can impact matching scores. The focus of this paper is the pose problem which remains largely overlooked in most real-world applications. Specifically, we focus on one-to-one matching scenarios where a query face image of a random pose is matched against a set of gallery images. We propose a method that relies on two fundamental components: (a) A 3D modeling step to geometrically correct the viewpoint of the face. For this purpose, we extend a recent technique for efficient synthesis of 3D face models called 3D Generic Elastic Model. (b) A sparse feature extraction step using subspace modeling and ℓ1-minimization to induce pose-tolerance in coefficient space. This in return enables the synthesis of an equivalent frontal-looking face, which can be used towards recognition. We show significant performance improvements in verification rates compared to commercial matchers, and also demonstrate the resilience of the proposed method with respect to degrading input quality. We find that the proposed technique is able to match non-frontal images to other non-frontal images of varying angles.
Analysis of circulating microRNAs in patients with repaired Tetralogy of Fallot with and without heart failure (2017)

Altered expression levels of circulating miRNAs were found in TOF patients late after surgical repair and are different to those seen in the right ventricular myocardium of infants with TOF. Expression levels of miR-421, miR-1233-3p and miR-625-5p are lower in TOF patients with symptomatic right heart failure and thus may indicate disease progression in these patients.
A novel approach to predict the instabilities and analyze the dynamics of a single phase bidirectional boost converter (2003)

We develop an analytical map for a single phase bidirectional boost converter. This map enables the analysis of the dynamics of the converter faster and without any convergence problems. For the closed-loop converter, we show how instabilities can occur on the slow and fast scales. Conventional analyses based on averaged models can not predict the fast-scale instability because such models do not account for the switching frequency ripple.
A Patent Review on SARS Coronavirus Main Protease (3CL<sup>pro</sup>) Inhibitors (2021)

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an unprecedented global health emergency causing more than 4.2 million fatalities as of 30 July 2021. Only three antiviral therapies have been approved or granted emergency use authorization by the FDA. The SARS-CoV-2 3CL protease (3CL<sup>pro</sup> ) is deemed an attractive drug target as it plays an essential role in viral polyprotein processing and pathogenesis, although no inhibitors have been approved. This patent review discusses SARS coronavirus 3CL<sup>pro</sup> inhibitors that have been filed up to 30 July 2021, giving an overview on the types of inhibitors that have generated commercial interest, especially amongst drug companies. Insights into the common structural motifs required for active site binding is also discussed.
Intelligent realisation of ground energy (2008)

There is a need to reduce the economic cost of the energy geostructures and increase the efficiency of such systems, which will also rationalise the environmental impact.
Dynamics of the SPRY domain–containing SOCS box protein 2: Flexibility of key functional loops (2006)

The SPRY domain was identified originally as a sequence repeat in the dual-specificity kinase splA and ryanodine receptors and subsequently found in many other distinct proteins, including more than 70 encoded in the human genome. It is a subdomain of the B30.2/SPRY domain and is believed to function as a protein-protein interaction module. Three-dimensional structures of several B30.2/SPRY domain-containing proteins have been reported recently: murine SSB-2 in solution by NMR spectroscopy, a Drosophila SSB (GUSTAVUS), and human PRYSPRY protein by X-ray crystallography. The three structures share a core of two antiparallel beta-sheets for the B30.2/SPRY domain but show differences located mainly at one end of the beta-sandwich. Analysis of SSB-2 residues required for interactions with its intracellular ligands has provided insights into B30.2/SPRY binding specificity and identified loop residues critical for the function of this domain. We have investigated the backbone dynamics of SSB-2 by means of Modelfree analysis of its backbone (15)N relaxation parameters and carried out coarse-grained dynamics simulation of B30.2/SPRY domain-containing proteins using normal mode analysis. Translational self-diffusion coefficients of SSB-2 measured using pulsed field gradient NMR were used to confirm the monomeric state of SSB-2 in solution. These results, together with previously reported amide exchange data, highlight the underlying flexibility of the loop regions of B30.2/SPRY domain-containing proteins that have been shown to be important for protein-protein interactions. The underlying flexibility of certain regions of the B30.2/SPRY domain-containing proteins may also contribute to some apparent structural differences observed between GUSTAVUS or PRYSPRY and SSB-2.
Scrambled Translation Problem: A Problem of Denoising UNMT (2019)

In this paper, we identify an interesting kind of error in the output of Unsupervised Neural Machine Translation (UNMT) systems like \textit{Undreamt}(footnote). We refer to this error type as \textit{Scrambled Translation problem}. We observe that UNMT models which use \textit{word shuffle} noise (as in case of Undreamt) can generate correct words, but fail to stitch them together to form phrases. As a result, words of the translated sentence look \textit{scrambled}, resulting in decreased BLEU. We hypothesise that the reason behind \textit{scrambled translation problem} is 'shuffling noise' which is introduced in every input sentence as a denoising strategy. To test our hypothesis, we experiment by retraining UNMT models with a simple \textit{retraining} strategy. We stop the training of the Denoising UNMT model after a pre-decided number of iterations and resume the training for the remaining iterations -- which number is also pre-decided -- using original sentence as input without adding any noise. Our proposed solution achieves significant performance improvement UNMT models that train conventionally. We demonstrate these performance gains on four language pairs, \textit{viz.}, English-French, English-German, English-Spanish, Hindi-Punjabi. Our qualitative and quantitative analysis shows that the retraining strategy helps achieve better alignment as observed by attention heatmap and better phrasal translation, leading to statistically significant improvement in BLEU scores.
Automatic design of parallel implementations of DSP algorithms (2002)

An integrated system is presented combining a rule-based symbolic code simplification system and a fine-grain code scheduler for a multiprocessor based on a ring/mesh of commercial single-chip digital signal processing (DSP) processors. The code simplification component uses a priori information to direct the application of symbolic simplification rules to local or global code segments of the original program. The code generation includes graph parsing, optional blocking, and code scheduling with partial backtracking. Resource allocation is incorporated with operation scheduling to increase the total performance of the practical system. The integrated system can implement many DSP algorithms, generating very efficient code for a variety of DSP processor configurations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
P0038WATER RESTRICTION INDUCES THE SHORTENING OF PRIMARY CILIA IN KIDNEY TUBULAR CELLS (2020)

Abstract Background and Aims The primary cilia play a key role in the maintenance of cell homeostasis by sensing and transducing extracellular signals into the cell and are associated with several kidney diseases including ADPKD. Here, we investigated whether water restriction affects the length of primary cilia of kidney tubule cells and its underlying mechanisms. Method Some mice were not supplied with water for 2 days and then the length of primary cilia were determined by immunostaining using acetylated-α-tubulin (ac-α-tubulin) antibody. Madin-Darby canine kidney (MDCK) cells were exposed to high concentration of NaCl or mannitol and the lengths of primary cilia were determined under microscope. Results Water restriction shortened primary cilia length in kidney tubular cells along with the increase of urine osmolality. Water restriction lowered the expression of acetylated-α-tubulin (ac-α-tubulin), EXOC5, one of the components of exocyst complex, and α-tubulin transferase in the kidney. In MDCK cells, high concentration of NaCl or mannitol treatments shortened primary cilia length and decreased the expression of ac-α-tubulin, EXOC5, and α-tubulin transferase. Conclusion These findings demonstrate that water restriction induces the shortening of primary ciliua in kidney tubule cells along with increased urine osmolality, suggesting that primary cilia are involved in the urine concentric process.
Biomechanics after spinal decompression and posterior instrumentation (2023)

The amount of posterior decompression significantly impacts ROM of the lumbar spine. The here performed biomechanical study allows creation of a simplified rule of thumb: Increases in segmental ROM of approximately 10%, 20%, and 50% can be expected after unilateral laminotomy, midline decompression, and nucleotomy, respectively. Instrumentation decreases ROM by approximately 80% in bending moments and accompanied decompression procedures only minorly destabilize the instrumentation construct.
Estimation of spatio-temporal temperature evolution during laser spot melting using in-situ dynamic x-ray radiography (2023)

Understanding the spatio-temporal evolution of thermal gradient (G) at and velocity (R) of the solid-liquid and liquid-vapor interfaces is critical for the control of site-specific microstructures in additive manufacturing. In-situ dynamic x-ray radiography (DXR) has been used in recent years to probe the evolution of R with high spatial and temporal resolutions. However, the current methods used to measure the temperature (and therefore, G) are inadequate for sub-melt-pool surface measurement (e.g. thermography) or have lower resolution or limited field-of-view (e.g. x-ray diffraction). In this study, we demonstrate a novel approach to estimate the sub-surface temperature distribution and its time evolution with significantly higher resolutions using DXR data. This methodology uses the Beer-Lambert's law as a physical basis and is demonstrated using an in-situ laser spot-melting experiment on Ti-6Al-4V alloy.
Midline Craniotomy for Resection of Cavernous Malformation: 2-Dimensional Operative Video (2019)

This patient presented with a cavernous malformation in the inferior posterior third ventricle extending into the aqueduct. The patient was positioned supine on the operating room table with the head rotated into the horizontal plane. The choroidal fissure is opened lateral to the choroid plexus. This technique allows for the choroid plexus to serve as protection against forniceal manipulation. Rigid retraction was applied to the cerebral falx and corpus callosum to permit aqueductal visualization. The lighted instruments are paramount for adequate visualization of the third ventricle and during dissection of the lesion. Intraoperative visualization and postoperative imaging confirm gross total resection of the lesion. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute.
Field emission characterization of silicon tip arrays coated with GaN and diamond nanoparticle clusters (2003)

Wide band-gap materials show promise for applications in coating of field emission tips. Recently nanocrystalline hexagonal GaN crystallites as small as 12 nm average diameter have been formed using reactive laser ablation of gallium metal in nitrogenating ambient [T. J. Goodwin et al., Appl. Phys. Lett. 70, 3122 (1997)]. In this article we investigated the performance of ungated emitters with and without surface coating. Silicon tip arrays are coated by dielectrophoresis of gallium nitride nanoparticles or nanocrystalline diamond clusters from an ethanol suspension. The emitters were evaluated and compared before and after the surface treatment using SEM image and I–V measurements in the diode configuration. The results suggest that the emitters benefit from coating the surface with nanocrystalline diamond clusters in terms of reduction in the turn on voltage by 100 V and increase uniformity in emission during low voltage operation. The long-term emission stability for both types of the coated cathodes was studied over a period of 90 h. The emitters coated with GaN nanoparticle clusters show a significant improvement in the current fluctuation from 150% (for untreated cathodes) to 50%.
RH5–Basigin interaction plays a major role in the host tropism of <i>Plasmodium falciparum</i> (2013)

Plasmodium falciparum, the cause of almost all human malaria mortality, is a member of the Laverania subgenus which infects African great apes. Interestingly, Laverania parasites exhibit strict host specificity in their natural environment: P. reichenowi, P. billcollinsi, and P. gaboni infect only chimpanzees; P. praefalciparum, P. blacklocki, and P. adleri are restricted to gorillas, and P. falciparum is pandemic in humans. The molecular mechanism(s) responsible for these host restrictions are not understood, although the interaction between the parasite blood-stage invasion ligand EBA175 and the host erythrocyte receptor Glycophorin-A (GYPA) has been implicated previously. We reexamined the role of the EBA175-GYPA interaction in host tropism using recombinant proteins and biophysical assays and found that EBA175 orthologs from the chimpanzee-restricted parasites P. reichenowi and P. billcollinsi both bound to human GYPA with affinities similar to that of P. falciparum, suggesting that the EBA175-GYPA interaction is unlikely to be the sole determinant of Laverania host specificity. We next investigated the contribution of the recently discovered Reticulocyte-binding protein Homolog 5 (RH5)-Basigin (BSG) interaction in host-species selectivity and found that P. falciparum RH5 bound chimpanzee BSG with a significantly lower affinity than human BSG and did not bind gorilla BSG, mirroring the known host tropism of P. falciparum. Using site-directed mutagenesis, we identified residues in BSG that are responsible for the species specificity of PfRH5 binding. Consistent with the essential role of the PfRH5-BSG interaction in erythrocyte invasion, we conclude that species-specific differences in the BSG receptor provide a molecular explanation for the restriction of P. falciparum to its human host.
Abstract 3133: Apoptosis signal-regulating kinase 1 and cyclin D1 compose a positive feedback loop contributing to tumor growth in gastric cancer (2011)

Abstract Gastric cancer is a common cancer worldwide, associated with a high mortality despite its declining incidence in recent decades. Although the role of H. pylori in causing mucosal effects has been investigated, which molecular signal(s) initiate the program of irreversible transformation remain unclear, and thus molecular targeting therapies for GC have not been well established. Mitogen-activated protein kinase (MAPK) pathways regulate multiple cellular functions and have been demonstrated to be highly active in many types of human cancers, and we have previously reported that c-Jun-N-terminal kinase 1 (JNK1) is important for gastric tumorigenesis. Apoptosis signal-regulating kinase 1 (ASK1) is an upstream MAPK known to be involved in apoptosis, inflammation, and carcinogenesis. In the current study, we investigated the role of ASK1 in the development of gastric cancer. In human gastric cancer specimens, we observed increased ASK1 expression compared to non-tumor epithelium, while we found no difference between colon cancer and non-tumor colon epithelium. Using the chemically induced murine gastric tumorigenesis model, we observed increased tumor ASK1 expression, and ASK1 knockout mice displayed both a lower number and smaller tumor size compared to wild-type mice. In gastric cancer cell lines, immunoprecipitation analysis revealed constitutive ASK1 activation in several cell lines. ASK1 siRNA inhibited cell proliferation through the accumulation of cells in G1 phase of the cell cycle, and reduced cyclin D1 expression in gastric cancer cells, while these effects were uncommon in other cancer cells, suggesting that the ASK1-dependent regulation of the cyclin D1 level and cellular proliferation is specific to gastric cancer. Overexpression of ASK1 induced the transcription of cyclin D1 through AP-1 activation in a kinase-dependent manner. In addition, we found that the expression of ASK1 was elevated following epidermal growth factor (EGF) or Helicobacter pylori (H.pylori) treatment in control cells but not in cyclin D1 silencing cells. Overexpression of cyclin D1 enhanced phosphorylation of Rb, followed by the increase in ASK1 expression. Chromatin immunoprecipitation (ChIP) assay showed that cyclin D1 expression increase E2F1 binding to ASK1 promoter, suggesting that the levels of ASK1 were regulated by cyclin D1 through the Rb-E2F pathway. Exogenous ASK1 induced cyclin D1 expression, followed by an elevated expression of endogenous ASK1. These results indicate an autoregulatory mechanism of ASK1 in the development of gastric cancer. Through targeting this positive feedback loop, ASK1 may present a potential therapeutic target for the treatment of advanced gastric cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3133. doi:10.1158/1538-7445.AM2011-3133
Realization of a Safe and Secure Society using ICT in Shiojiri-City, Nagano Prefecture, Japan (2015)

For some time, we have been working toward the “Realization of a Safe and Secure Society using ICT in Shiojiri-City, Nagano Prefecture.” This is a project comprised of two phases: information gathering, and dissemination of information. For information gathering, we are developing systems to confirm the whereabouts of children and the elderly, who are vulnerable in disasters, and systems to gather information on the situation in mountainous regions, rivers etc. For dissemination of information, we are developing systems using broadcast technology for disseminating information to residents, such as disaster information and evacuation warnings derived from the gathered information. This presentation will describe the project goals, the background of the project thus far, and an overview of the developed system. The current situation and plans for the future will also be discussed.
On the uniqueness of maximal operators for ergodic flows (2002)

The uniqueness theorem for the ergodic maximal operator is proved in the continuous case.
Chronic lymphocytic leukemia with del(17p13.1): a distinct clinical subtype requiring novel treatment approaches. (2012)

Chronic lymphocytic leukemia (CLL) is a very heterogeneous disease with significant variation in clinical presentation, time to disease progression, survival, and aggressiveness of clinical course. A subgroup of patients who have been repeatedly identified as having a poor response to therapy are those with del(17p13.1)--identified by either interphase cytogenetics or other comparable strategies. Although there has been much progress over the past few years in the development of new therapeutic targets for CLL patients, this subgroup has continued to lag behind others. Because of the poor response or significant therapy-related toxicity experienced by patients with del(17p13.1)--and the small number of these patients included in clinical trials--current guidelines are unable to provide suggestions for the care of newly diagnosed, symptomatic but untreated patients (as well as relapsed patients) in this subgroup on account of the modest amount of evidence. However, novel agents are on the horizon that appear to be significantly more effective in this patient population, and these will likely shape the standard of care for these patients in the future.
Long-term safety and efficacy of breast biopsy markers in clinical practice (2020)

<b>Objective</b>: Percutaneous breast and axillary core biopsy followed by marker placement are integral parts of a breast imager's practice benefiting both patients and clinicians. Marker placement is the standard to facilitate future care. The purpose of this study is to characterize the safety and performance of MammoMARK, CorMARK, and HydroMARK biopsy markers by evaluating device-related adverse events, device deficiencies, and long-term safety.<b>Methods</b>: A retrospective review of three radiology practices identified patients who underwent image-guided breast or axillary biopsies followed by marker placement between 1 January 2012 and 1 January 2017. Medical records were reviewed with adverse events related to marker placement and use recorded.<b>Results</b>: 768 markers were placed with three (0.4%) events recorded. Two device deficiencies and one non-serious adverse event occurred in three patients. Device deficiency events involved user errors deploying the markers, one to inability to locate the marker on post-biopsy imaging, and the second to misplacement relative to biopsy target. One non-serious adverse event involved inability to locate/retain the marker in a surgically resected specimen. No serious adverse events were reported.<b>Conclusion</b>: Placement of breast biopsy markers is safe with minimal associated risks. Issues related to device malfunction, durability, reliability, safety, or performance were not reported.