gebhart/patrepeval huggingface dataset:
Privacy-preserving string search for genome sequences with FHE bootstrapping optimization (2016)

Privacy-preserving string search is a crucial task for analyzing genomics-driven big data. In this work, we propose a cryptographic protocol that uses Fully Homomorphic Encryption (FHE) to enable a client to search on a genome sequence database without leaking his/her query to the server. Though FHE supports both addition and multiplication over encrypted data, random noise inside ciphertexts grows with every arithmetic operation especially multiplication, which results in incorrect decryption when the noise amount exceeds its threshold called level. There are two approaches to avoid the incorrect decryption: one is setting the sufficient level that assures correct decryption within the limited number of operations, and the other is resetting the noise by the method called bootstrapping. It is important to find an optimal balance between overhead caused by the level and overhead caused by the bootstrapping, since using higher level deteriorates the performance of all the arithmetic operations, while the more number of bootstrappings causes more expensive overhead. In this study, we propose an efficient approach to minimize the number of bootstrappings while reducing the level as much as possible. Our experimental result shows that it runs at most 10 times faster than a naïve approach.
Protective Roles of O‐GlcNAc in Neurodegenerative Diseases (2021)

O‐linked N‐acetylglucosamine (O‐GlcNAc) is an abundant form of protein O‐glycosylation found in the nucleus, cytoplasm, and mitochondria of all multicellular eukaryotes. This modification is found on several hundred proteins but is surprisingly regulated by only two enzymes; the glycosyltransferase O‐GlcNAc transferase (OGT) and the glycoside hydrolase O‐GlcNAcase (OGA). Because the substrate of OGT is derived from glucose, the levels of O‐GlcNAc within cells reflect environmental glucose availability. O‐GlcNAc has also emerged as part of a coordinated response to cellular stresses and levels of this modification increase markedly on exposure to diverse stresses ranging from heat shock to oxidative stress. These observations have stimulated interest in the potential protective roles of increased O‐GlcNAc in a range of tissues including in brain, where impaired nutrient utilization has been linked to various neurodegenerative diseases. Remarkably, brain permeable small molecule inhibitors of OGA have been shown to be surprisingly well tolerated in a range of animal models. Moreover, pharmacological agents that increase O‐GlcNAc levels in the brains of various transgenic models of Alzheimer Disease (AD) strikingly reduce the progression of disease pathology and neurodegeneration. While these effects have been shown to be remarkably reproducible, and OGA inhibitors have now been found to be generally well tolerated in early clinical trials, the mechanisms by which O‐GlcNAc protect against these pathologies and neurodegeneration remain less clear. Here we will discuss new advances in the biochemistry of OGA inhibitors, efforts to create improved inhibitors, and the protective effects of OGA in transgenic models of neurodegenerative diseases. Finally, we will discuss recent progress on various possible protective mechanisms by which increased O‐GlcNAc levels confer protection against various neurodegenerative diseases ranging from blockade of aggregation of toxic proteins to the induction of autophagy.
Developments of (Ba,Na)Fe 2 As 2 and CaKFe 4 As 4 HIP round wires (2020)

Abstract With excellent superconducting properties such as high T c , large H c2 , small anisotropy, and large J c , developments of superconducting wires and tapes of iron-based superconductors (IBSs) have been undertaken with promising results. So far, K-doped 122-type IBSs have been mainly developed for such purposes. Here, efforts to fabricate Na-doped 122-type IBS, (Ba,Na)Fe 2 As 2 , are presented. With the help of hot isostatic pressing (HIP) process, excellent J c characteristics of up to 44 kA cm −2 at 4.2 K under 100 kOe have been achieved. Detailed characterizations of (Ba,Na)Fe 2 As 2 HIP round wire are presented. On the other hand, discoveries of new IBSs continue, with CaKFe 4 As 4 as one of recent examples. CaKFe 4 As 4 belongs to a new family of IBSs with 1144 structure, where Ca and K occupy the Ba site in BaFe 2 As 2 alternately along the c -axis. Studies on CaKFe 4 As 4 single crystals have demonstrated moderately large J c with peculiar anisotropic properties related to the presence of novel planar defects. We have also fabricated HIP round wires of CaKFe 4 As 4 , and reported their basic characterizations. Despite the instability of CaKFe 4 As 4 at low temperatures, J c values at 4.2 K close to 100 kA cm −2 at self-field and 7.6 kA cm −2 at 100 kOe are achieved. Attempts to introduce defects into CaKFe 4 As 4 single crystals, chemically by Co substitution and physically by proton irradiation, are attempted, and the effects are compared. Attempts to fabricate Co-doped CaKFe 4 As 4 HIP round wires with limited success are also reported.
Immobilization Modulates Macrophage Accumulation in Tendon-Bone Healing (2008)

Tendon-to-bone healing occurs by formation of a fibrous, scar tissue interface rather than regeneration of a normal insertion. Because inflammatory cells such as macrophages lead to formation of fibrous scar tissue, we hypothesized immobilization would allow resolution of acute inflammation and result in improved tendon-bone healing. We reconstructed the ACL of 60 Sprague-Dawley rats using a tendon autograft. An external fixation device was used to immobilize the surgically treated knee in 30 rats. We evaluated tendon-bone interface width, collagen fiber continuity, and new osteoid formation histologically. Immunohistochemistry was used to localize ED1+ and ED2+ macrophages at the tendon-bone interface at 2 and 4 weeks. Biomechanical testing was performed at 4 weeks. Interface width was smaller and collagen fiber continuity was greater in the immobilized group. Immobilized animals exhibited fewer ED1+ macrophages at the healing interface at 2 and 4 weeks. In contrast, there were more ED2+ macrophages at the interface in the immobilized group at 2 weeks. Failure load and stiffness were similar between groups at 4 weeks. The data suggest early immobilization diminishes macrophage accumulation and may allow improved tendon-bone integration.
Characterization of the interactions between double-stranded RNA and the double-stranded RNA binding domain of the interferon induced protein kinase. (1994)

The interferon-inducible protein kinase, PKR, requires double-stranded (ds) RNA for its activation. We have previously mapped its dsRNA-binding domain (DRBD) to the amino terminal 170 residues (Patel and Sen, 1992). In the present study, we have characterized in detail the interactions between dsRNA and DRBD. For this purpose, DRBD was produced in bacteria as a polyhistidine-tagged protein and purified by affinity chromatography. A polyclonal antibody was raised against purified DRBD. For studying dsRNA-DRBD interactions, a Northwestern assay and an electrophoretic mobility shift assay (EMSA) using a radiolabeled in vitro transcribed 82 bp dsRNA probe was developed. The antiserum reacted with both DRBD and PKR but did not prevent their interactions with dsRNA. DRBD, on the other hand, blocked the activation of PKR by dsRNA. DRBD and the dsRNA probe formed multimeric complexes which were separable by EMSA. The antibody could interact with these complexes and supershift their mobility. Competition with unlabeled dsRNA revealed that the dimeric DRBD-dsRNA complex was much more stable than the monomeric complex. Similar competition assays using 11 different synthetic and natural RNA molecules revealed that only authentic dsRNA molecules could effectively compete with the probe for binding DRBD in a sequence-independent fashion.
Toward complete space-time reconstruction of light pulses (2012)

We introduce generic approach for complete space-time characterization of the light pulses. Measured spectrally resolved wavefront across one plane and knowledge of temporal profile at one point in space allow complete space-time reconstruction of the pulse.
Humoral response rate and predictors of response to BNT162b2 mRNA COVID19 vaccine in patients with multiple myeloma (2021)

Multiple myeloma (MM) patients are at excess risk for clinically significant COVID19 infection. BNT162b2 mRNA COVID19 (BNT162b2) vaccine provides effective protection against COVID19 for the general population, yet its effect in MM patients may be compromised due to disease and therapy-related factors and was not yet evaluated. This single-centre prospective study included MM patients tested for serological response 14-21 days post second vaccine. Vaccinated healthy volunteers served as controls. In all, 171 MM patients, median age 70 (38-94) were included; 159 active MM and 12 smouldering myeloma (SMM). Seropositive response rate (median titer) was 76% (91 U/ml) in active MM patients vs 98% (992 U/ml) in the 64 controls (P < 0·0001), and 100% (822 U/ml) in SMM patients. Multivariate analysis revealed older age (P = 0·009), exposure to ≥4 novel anti-myeloma drugs (P = 0·02) and hypogammaglobulinaemia (P = 0·002) were associated with lower response rates. None of the novel agents significantly decreased response rate, whereas daratumumab trended towards reduced response (P = 0·08). Adverse events occurred in 53% and 55% of the MM patients and controls, respectively, all transient grade 1-2. In conclusion, BNT162b2 vaccine was safe and provided a high seropositivity rate in MM patients, independent of treatment type. Older, hypogammaglobulinaemic and heavily pretreated patients had lower response rates.
Systemic thrombolysis and endovascular thrombectomy in severe acute ischemic stroke after dabigatran reversal with idarucizumab (2018)

Patients presenting with an acute ischemic stroke despite dabigatran therapy (last intake <24 h or unknown) should be evaluated for reversal by idarucizumab, making them eligible for safe and effective intravenous thrombolysis. It has been shown to be feasible, well-tolerated, and easy to manage in an emergency room or stroke unit.
Recommendation-Based De-identification: A Practical Systems Approach towards De-identification of Unstructured Text in Healthcare (2012)

In healthcare, de-identification is fast becoming a service that is indispensable when medical data needs to be used for research and secondary use purposes. Currently, this process is done either manually, by human agent, or by an automated software algorithm. Both approaches have shortcomings. Here, we introduce a framework for enhancing the outcome of the current modes of executing a de-identification service. This paper presents the steps taken in conceiving and building a privacy framework and tool that improves the service of de-identification. Further, we test the usefulness and applicability of this system through a study with HIPAA-trained experts.
Higher integrability for vector-valued parabolic quasi-minimizers on metric measure spaces (2015)

We establish local higher integrability estimates for upper gradients of vector-valued parabolic quasi-minimizers in metric measure spaces, satisfying a doubling property and supporting a weak Poincaré inequality.
Toroidal Structure and DNA Cleavage by the CRISPR-Associated [4Fe-4S] Cluster Containing Cas4 Nuclease SSO0001 from Sulfolobus solfataricus (2013)

Cas4 proteins, a core protein family associated with the microbial system of adaptive immunity CRISPR, are predicted to function in the adaptation step of the CRISPR mechanism. Here we show that the Cas4 protein SSO0001 from the archaeon Sulfolobus solfataricus has metal-dependent endonuclease and 5'→3' exonuclease activities against single-stranded DNA, as well as ATP-independent DNA unwinding activity toward double-stranded DNA. The crystal structure of SSO0001 revealed a decameric toroid formed by five dimers with each protomer containing one [4Fe-4S] cluster and one Mn(2+) ion bound in the active site located inside the internal tunnel. The conserved RecB motif and four Cys residues are important for DNA binding and cleavage activities, whereas DNA unwinding depends on several residues located near the [4Fe-4S] cluster. Our results suggest that Cas4 proteins might contribute to the addition of novel CRISPR spacers through the formation of 3'-DNA overhangs and to the degradation of foreign DNA.
Surface-enhanced spectroscopy: Toward practical analysis probe (2018)

Surface-enhanced spectroscopy (SES) is a consequence of extreme electromagnetic fields and chemical interactions near a surface. SES is highly sensitive and selective and has been exploited in chemistry, physics, biology, and medicine. It is a rapidly developing technique and is expected to become an important analysis tool. This review introduces theories and concepts of SES techniques including surface-enhanced (SE) Raman scattering, SE infrared absorption, SE chiroptical spectroscopy, and SE fluorescence. Then recent research and applications are discussed to indicate current challenges and future directions.
Effect of seed priming with NaCl on maize germination under different saline conditions (2011)

-1 and priming treatments were 0.0, 0.5 and 1.0 M NaCl. Shoot dry weight (SDW), shoot length (SL), leaves number (LN), leaf area (LA), chlorophyll (Chl) and ion leakage (IL) were measured. Effects of salinity and seed priming on shoot dry weight, shoot length, leaves number, leaf area, chlorophyll and ion leakage were significant (P < 0.01). Increasing salinity up to 12 dS.m -1 negatively influenced all traits except ion leakage and the amount of reduction for the mentioned traits were 75.67, 52.25, 25, 69.97 and 21.17%, respectively, compared to the control. In the case of ion leakage, it was 3.03 times of control. Seed priming compensated the negative effects of salinity on the traits and all of them positively responded to seed priming. Based on these results seed priming with NaCl may be considered as a reliable procedure to increase the maize salinity tolerance.
Optical and Electrical Improvement of Rear Side ITO for Heterojunction Back Contact Solar Cells (2014)

In this paper, the electrical and optical characteristics of the Indium-Doped Tin Oxide (ITO) are tuned in order to design an ITO-based spacer between the a-Si:H and the metal contact suited for Amorphous / Crystalline Heterojunction interdigitated Back Contact Solar Cells (a-Si:H / c-Si HJ i-BC). ITO carrier concentration, mobility, resistivity, extinction coefficient, and work function, as well as the ITO / a-Si:H specific contact resistances are evaluated as a function of O2 relative flow rate during ITO deposition. An ITO having carrier concentration of 4.5x1019 cm-3, mobility of 20.2 cm2/(V.s) and resistivity of 6.24 mΩ.cm is found to be an optimum leading to ITO / a-Si:H(p/i) and ITO / a-Si:H(n/i) specific contact resistances values of 0.6 Ω.cm2 and 0.1 Ω.cm2 respectively and a RS reflectance of 58% at 1200nm when integrated in Silver / ITO / a-Si:H / c-Si(textured) test structures.
Racemase activity effected by two dehydrogenases in sulfolactate degradation by Chromohalobacter salexigens: purification of (S)-sulfolactate dehydrogenase (2009)

Chromohalobacter salexigens DSM 3043, whose genome has been sequenced, is known to degrade (R,S)-sulfolactate as a sole carbon and energy source for growth. Utilization of the compound(s) was shown to be quantitative, and an eight-gene cluster (Csal_1764-Csal_1771) was hypothesized to encode the enzymes in the degradative pathway. It comprised a transcriptional regulator (SuyR), a Tripartite Tricarboxylate Transporter-family uptake system for sulfolactate (SlcHFG), two sulfolactate dehydrogenases of opposite sulfonate stereochemistry, namely novel SlcC and ComC [(R)-sulfolactate dehydrogenase] [EC 1.1.1.272] and desulfonative sulfolactate sulfo-lyase (SuyAB) [EC 4.4.1.24]. Inducible reduction of 3-sulfopyruvate, inducible SuyAB activity and induction of an unknown protein were detected. Separation of the soluble proteins from induced cells on an anion-exchange column yielded four relevant fractions. Two different fractions reduced sulfopyruvate with NAD(P)H, a third yielded SuyAB activity, and the fourth contained the unknown protein. The latter was identified by peptide-mass fingerprinting as SlcH, the candidate periplasmic binding protein of the transport system. Separated SuyB was also identified by peptide-mass fingerprinting. ComC was partially purified and identified by peptide-mass fingerprinting. The (R)-sulfolactate that ComC produced from sulfopyruvate was a substrate for SuyAB, which showed that SuyAB is (R)-sulfolactate sulfo-lyase. SlcC was purified to homogeneity. This enzyme also formed sulfolactate from sulfopyruvate, but the latter enantiomer was not a substrate for SuyAB. SlcC was obviously ( S)-sulfolactate dehydrogenase.
Hepatocyte growth factor twenty years on: Much more than a growth factor (2011)

Liver regeneration depends on the proliferation of mature hepatocytes. In the 1980s, the method for the cultivation of mature hepatocytes provided an opportunity for the discovery of hepatocyte growth factor (HGF) as a protein that is structurally and functionally different from other growth factors. In 1991, the scatter factor, tumor cytotoxic factor, and 3-D epithelial morphogen were identified as HGF, and Met tyrosine kinase was identified as the receptor for HGF. Thus, the connection of apparently unrelated research projects rapidly enriched the research on HGF in different fields. The HGF-Met pathway plays important roles in the embryonic development of the liver and the placenta, in the migration of myogenic precursor cells, and in epithelial morphogenesis. The use of tissue-specific knockout mice demonstrated that in mature tissues the HGF-Met pathway plays a critical role in tissue protection and regeneration, and in providing less susceptibility to chronic inflammation and fibrosis. In various injury and disease models, HGF promotes cell survival, regeneration of tissues, and suppresses and improves chronic inflammation and fibrosis. Drug development using HGF has been challenging, but extensive preclinical studies to address its therapeutic effects have provided significant results sufficient for the development of HGF as a biological drug in the regeneration-based therapy of diseases. Clinical trials using recombinant human HGF protein, or HGF genes, are in progress for the treatment of diseases.
An Experimental Study of the Effect of Cylinder Bore Finish on Engine Oil Consumption (1995)

&lt;div class="htmlview paragraph"&gt;Past oil consumption reduction efforts were motivated by operating cost, petroleum conservation, or customer quality perception concerns. Recent efforts have been driven by exhaust catalyst poisoning considerations. The need to certify emissions to a higher mileage level and optimization efforts on the emission control systems have resulted in higher objectives for oil control.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper focuses on one important factor in the control of lubrication oil consumption in internal combustion engines. Previous studies have related bore finish to oil consumption through either theoretical or experimental techniques. In this study, a mathematical model is derived statistically from experimental data utilizing regression analysis and a new transient radiotracer oil consumption measurement technique. The model predicts oil consumption levels expected with variations in cylinder bore finish, and suggests the important surface finish parameters to specify and control for minimum oil consumption.&lt;/div&gt;
Chapter 18. The co-ordination chemistry of macrocyclic ligands (1999)

I. A. Fallis, Annu. Rep. Prog. Chem., Sect. A: Inorg. Chem., 1999, 95, 313 DOI: 10.1039/A804898C
A partition function algorithm for interacting nucleic acid strands (2009)

Supplementary data are avaliable at Bioinformatics online.
Two key events associated with a transposable element burst occurred during rice domestication (2018)

Abstract Transposable elements shape genome evolution through periodic bursts of amplification. In this study we exploited knowledge of the components of the mPing/Ping/Pong TE family in four rice strains undergoing mPing bursts to track their copy numbers and distribution in a large collection of genomes from the wild progenitor Oryza rufipogon and domesticated Oryza sativa (rice). We characterized two events that occurred to the autonomous Ping element and appear to be critical for mPing hyperactivity. First, a point mutation near the end of the element created a Ping variant ( Ping16A ) with reduced transposition. The proportion of strains with Ping16A has increased during domestication while the original Ping (Ping16G) has been dramatically reduced. Second, transposition of Ping16A into a Stowaway element generated a locus ( Ping16A_Stow ) whose presence correlates with strains that have high mPing copies. Finally, demonstration that Pong elements have been stably silenced in all strains analyzed indicates that sustained activity of the mPing/Ping family during domestication produced the components necessary for the mPing burst, not the loss of epigenetic regulation.
Blanket Execution: Dynamic Similarity Testing for Program Binaries and Components (2018)

Matching function binaries—the process of identifying similar functions among binary executables—is a challenge that underlies many security applications such as malware analysis and patch-based exploit generation. Recent work tries to establish semantic similarity based on static analysis methods. Unfortunately, these methods do not perform well if the compared binaries are produced by different compiler toolchains or optimization levels. In this work, we propose <em>blanket execution</em>, a novel dynamic equivalence testing primitive that achieves complete coverage by overriding the intended program logic. Blanket execution collects the side effects of functions during execution under a controlled randomized environment. Two functions are deemed similar, if their corresponding side effects, as observed under the same environment, are similar too. We implement our blanket execution technique in a system called BLEX. We evaluate BLEX rigorously against the state of the art binary comparison tool BinDiff. When comparing optimized and un-optimized executables from the popular GNU coreutils package, BLEX outperforms BinDiff by up to 3:5 times in correctly identifying similar functions. BLEX also outperforms BinDiff if the binaries have been compiled by different compilers. Using the functionality in BLEX, we have also built a binary search engine that identifies similar functions across optimization boundaries. Averaged over all indexed functions, our search engine ranks the correct matches among the top ten results 77% of the time.
Hyaluronan is a natural and effective immunological adjuvant for protein-based vaccines (2021)

One of the main goals of vaccine research is the development of adjuvants that can enhance immune responses and are both safe and biocompatible. We explored the application of the natural polymer hyaluronan (HA) as a promising immunological adjuvant for protein-based vaccines. Chemical conjugation of HA to antigens strongly increased their immunogenicity, reduced booster requirements, and allowed antigen dose sparing. HA-based bioconjugates stimulated robust and long-lasting humoral responses without the addition of other immunostimulatory compounds and proved highly efficient when compared to other adjuvants. Due to its intrinsic biocompatibility, HA allowed the exploitation of different injection routes and did not induce inflammation at the inoculation site. This polymer promoted rapid translocation of the antigen to draining lymph nodes, thus facilitating encounters with antigen-presenting cells. Overall, HA can be regarded as an effective and biocompatible adjuvant to be exploited for the design of a wide variety of vaccines.