gebhart/patrepeval huggingface dataset:
Interplay between HIV-1 infection and host microRNAs (2011)

Using microRNA array analyses of in vitro HIV-1-infected CD4(+) cells, we find that several host microRNAs are significantly up- or downregulated around the time HIV-1 infection peaks in vitro. While microRNA-223 levels were significantly enriched in HIV-1-infected CD4(+)CD8(-) PBMCs, microRNA-29a/b, microRNA-155 and microRNA-21 levels were significantly reduced. Based on the potential for microRNA binding sites in a conserved sequence of the Nef-3'-LTR, several host microRNAs potentially could affect HIV-1 gene expression. Among those microRNAs, the microRNA-29 family has seed complementarity in the HIV-1 3'-UTR, but the potential suppressive effect of microRNA-29 on HIV-1 is severely blocked by the secondary structure of the target region. Our data support a possible regulatory circuit at the peak of HIV-1 replication which involves downregulation of microRNA-29, expression of Nef, the apoptosis of host CD4 cells and upregulation of microRNA-223.
Phase-shifting fringe projection system using freeform optics (2011)

Phase-shifting fringe projection is one of the most effective methods for shape measurement. Conventional systems are based on a projector imaging fringes into the measurement plane. These systems are mainly limited to the spectral range of visible light, as projectors in UV- or IR-range suffer from technical problems. However, for certain applications these spectral ranges can be of interest. We introduce a novel fringe projector based on beamshaping using a freeform mirror. The fringes in the measurement plane are generated by redistributing light with the freeform mirror. This projection system is wavelength-independent and highly energy efficient, which makes it suitable for applications in UV and IR spectral ranges. Additionally, a measurement field with axially very large dimension can be realized. We present here the system design as well as system simulation results, that demonstrate the principle of our novel approach.
Supplementary Figure 10 from Aging of Preleukemic Thymocytes Drives CpG Island Hypermethylation in T-cell Acute Lymphoblastic Leukemia (2023)

&lt;p&gt;Supplementary Figure 10&lt;/p&gt;
Review of Non-Destructive Methods for Rock Bolts Condition Evaluation (2023)

Rock bolts are one of the most effective and conventional support techniques widely used in underground mining and tunneling operations to stabilize excavations and jointed rock masses. External factors such as corrosion, overloading, and improper installation can weaken rock bolts, which could result in ground failure causing injury or loss of life and production. Monitoring the health condition of rock bolts will reduce the risk of accidents providing a safer environment for workers and equipment. This paper reviews monitoring methods currently used to assess the condition of installed rock bolts. Furthermore, we classify the surveyed techniques depending on the type of problems they attempt to solve. Presented are methods such as ultrasonics, fiber optics, piezoelectric, electromagnetics, impact echo, acoustic emission, and numerical algorithms. Each method is based on a unique physical principle that aids in evaluating corrosion and strain levels in the rock bolt. However, recent research to detect corrosion has primarily focused on rebar type of rock bolts used in concrete structures. Consequently, more research is needed to monitor the condition of the other types of rock bolts used in the industry such as cable bolts and split set bolts. In conclusion, the paper highlights various methods of studying rock bolt failure initiated by strain, corrosion, and improper installation of the grouts. It also explores the research advancement made for the study of rock bolt failure. This investigation is specifically beneficial to the mining and tunneling industry for better understanding and prediction of rock bolt failure.
Molecular engineering of cellulose-PCL bio-nanocomposite interface by reactive amphiphilic copolymer nanoparticles (2019)

Molecular engineering of cellulose-PCL bio-nanocomposite interface by reactive amphiphilic copolymer nanoparticles
Correction: Carbon nanotube-copper exhibiting metal-like thermal conductivity and silicon-like thermal expansion for efficient cooling of electronics (2019)

Correction for ‘Carbon nanotube-copper exhibiting metal-like thermal conductivity and silicon-like thermal expansion for efficient cooling of electronics’ by Chandramouli Subramaniam and Kenji Hata <italic>et al.</italic>, <italic>Nanoscale</italic>, 2014, <bold>6</bold>, 2669–2674.
Subcutaneous Immunization with Baculovirus Surface-Displayed Hemagglutinin of Pandemic H1N1 Influenza A Virus Induces Protective Immunity in Mice (2011)

The protective immunity of baculovirus displaying influenza virus hemagglutinin (BacHA) against influenza 2009 H1N1 virus infection in a murine model was investigated. The results showed that mice vaccinated with live BacHA or an inactive form of adjuvanted BacHA had enhanced specific antibody responses and induced protective immunity against 2009 H1N1 virus infection, suggesting the potential of baculovirus as a live or inactivated vaccine.
A Rapid 1H NMR Assay for Enantiomeric Excess of α-Substituted Aldehydes (2005)

In situ derivatization of a variety of alpha-substituted aldehydes via reaction with chiral amines allows convenient and efficient determination of enantiomeric excess. (1)H NMR analysis of the imine diastereomer ratio can be conducted immediately after the aldehyde and amine have been mixed. The results correlate well with ee values determined by more traditional (and slower) methods. This approach may be broadly applicable to alpha-substituted aldehydes. [reaction: see text]
MEMS oxygen transporter to treat retinal ischemia (2015)

For the first time, a paradigm shift in the treatment of retinal ischemia is proposed: providing localized supplemental oxygen to the ischemic tissue via an implanted MEMS device. A passive MEMS oxygen transporter is designed, built and tested in both artificial eye models and porcine cadaver eyes to confirm various hypotheses. The finite element modeling results predict that the proposed approach can treat complete retinal ischemia.
The IclR family of transcriptional activators and repressors can be defined by a single profile (2006)

In the last decade enormous advances in life sciences have been possible due to the information obtained from DNA sequencing projects. The optimal interpretation and analysis of genome sequence data requires the precise annotation and classification of proteins deduced from open reading frames, which is usually done with the help of family-specific signatures. Here we report a novel profile for the IclR type of transcriptional activators and repressors. In contrast to profiles for other families of transcriptional regulators, the new IclR profile is located outside the helix-turn-helix DNA-binding motif. We provide evidence that the new profile is more specific than any of the existing signatures for this family of regulators. More than 500 representatives of this family were identified with this profile. A database on bacterial regulators (http://www.bactregulators.org) was built to compile and regroup the sequences with the aid of the new profile.
ChemInform Abstract: Vanadium Mixed Oxide Catalysts for the Oxidative Coupling of Methane. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Ocular gene therapies in clinical practice: viral vectors and nonviral alternatives (2019)

Ocular gene therapy has entered into clinical practice. Although viral vectors are currently the best option to replace and/or correct genes, the optimal method to deliver these treatments to the retinal pigment epithelial (RPE) cells and/or photoreceptor cells remains to be improved to increase transduction efficacy and reduce iatrogenic risks. Beyond viral-mediated gene replacement therapies, nonviral gene delivery approaches offer the promise of sustained fine-tuned expression of secreted therapeutic proteins that can be adapted to the evolving stage of the disease course and can address more common nongenetic retinal diseases, such as age-related macular degeneration (AMD). Here, we review current gene therapy strategies for ocular diseases, with a focus on clinical stage products.
The SwitchWare Active Network Architecture (1998)

Active networks must balance the flexibility of a programmable network infrastructure against the safety and security requirements inherent in sharing that infrastructure. Furthermore, this balance must be achieved while maintaining the usability of the network. The SwitchWare active network architecture is a novel approach to achieving this balance using three layers: active packets, which contain mobile programs that replace traditional packets; active extensions, which provide services on the network elements and can be dynamically loaded; and a secure active router infrastructure, which forms a high-integrity base on which the security of the other layers depends. In addition to integrity checking and cryptography-based authentication, security in our architecture depends heavily on verification techniques from programming languages, such as strong type checking.
IonFlux: A Microfluidic Patch Clamp System Evaluated with Human Ether-à-go-go Related Gene Channel Physiology and Pharmacology (2011)

Ion channel assays are essential in drug discovery, not only for identifying promising new clinical compounds, but also for minimizing the likelihood of potential side effects. Both applications demand optimized throughput, cost, and predictive accuracy of measured membrane current changes evoked or modulated by drug candidates. Several competing electrophysiological technologies are available to address this demand, but important gaps remain. We describe the industrial application of a novel microfluidic-based technology that combines compounds, cells, and buffers on a single, standard well plate. Cell trapping, whole cell, and compound perfusion are accomplished in interconnecting microfluidic channels that are coupled to pneumatic valves, which emancipate the system from robotics, fluidic tubing, and associated maintenance. IonFlux™ is a state-of-the-art, compact system with temperature control and continuous voltage clamp for potential application in screening for voltage- and ligand-gated ion channel modulators. Here, ensemble recordings of the IonFlux system were validated with the human Ether-à-go-go related gene (hERG) channel (stably expressed in a Chinese hamster ovary cell line), which has established biophysical and pharmacological characteristics in other automated planar patch systems. We characterized the temperature dependence of channel activation and its reversal potential. Concentration response characteristics of known hERG blockers and control compounds obtained with the IonFlux system correlated with literature and internal data obtained on this cell line with the QPatch HT system. Based on the biophysical and pharmacological data, we conclude that the IonFlux system offers a novel, versatile, automated profiling, and screening system for ion channel targets with the benefit of temperature control.
STM-induced photon emission from self-assembled porphyrin molecules on a Cu(100) surface (2002)

An ultrahigh-vacuum scanning tunneling microscopy equipped with a conductive optical fiber tip and photon detector has been established to explore photon emission from a self-assembled monolayer (SAM) of Cu-tetra-[3,5-di-t-butylphenyl]porphyrin (Cu-TBPP) molecules on a Cu(100) surface. In a few nanometer scale areas, emitted photons from molecules induced by tunneling electrons were effectively collected within the near-field region through an apex of the conductive optical fiber tip. The photon emission can be attributed to the inelastic tunneling involving the optical fiber tip, the Cu-TBPP molecules, and the Cu(100) surface. We proposed two kinds of mechanisms in terms of the photon emission from a SAM of Cu-TBPP molecules on a Cu(100) surface. The quantum efficiency for molecular fluorescence induced by inelastic tunneling can be approximately estimated to be ∼3.0×10−6 photons per electron in the current experimental studies.
Solution Structure and Backbone Dynamics of the Holo Form of the Frenolicin Acyl Carrier Protein, (2003)

During polyketide biosynthesis, acyl carrier proteins (ACPs) perform the central role of transferring polyketide intermediates between active sites of polyketide synthase. The 4'-phosphopantetheine prosthetic group of a holo-ACP is a long and flexible arm that can reach into different active sites and provide a terminal sulfhydryl group for the attachment of acyl groups through a thioester linkage. We have determined the solution structure and characterized backbone dynamics of the holo form of the frenolicin acyl carrier protein (fren holo-ACP) by nuclear magnetic resonance (NMR). Unambiguous assignments were made for 433 hydrogen atoms, 333 carbon atoms, and 84 nitrogen atoms, representing a total of 94.6% of the assignable atoms in this protein. From 879 meaningful NOEs and 45 angle constraints, a family of 24 structures has been calculated. The solution structure is composed of three major alpha-helices packed in a bundle with three additional short helices in intervening loops; one of the short helices slowly exchanges between two conformations. Superposition of the major helical regions on the mean structure yields average atomic rmsd values of 0.49 +/- 0.09 and 0.91 +/- 0.08 A for backbone and non-hydrogen atoms, respectively. Although the three-helix bundle fold is conserved among acyl carrier proteins involved in fatty acid synthases and polyketide synthases, a detailed comparison revealed that ACPs from polyketide biosynthetic pathways are more related to each other in tertiary fold than to their homologues from fatty acid biosynthetic pathways. Comparison of the free form of ACPs (NMR structures of fren ACP and the Bacillus subtilis ACP) with the substrate-bound form of ACP (crystal structure of butyryl-ACP from Escherichia coli) suggests that conformational exchange plays a role in substrate binding.
MicroRNA miR-30 family regulates non-attachment growth of breast cancer cells (2013)

miR30-family regulates the growth of breast cancer cells in non-attachment conditions. This is the first analysis of target prediction in a whole family of microRNAs potentially involved in survival of putative BT-ICs.
Comparison of novel cleaning solutions with various chelating agents for post-CMP cleaning on poly-Si film (2001)

In this study, various cleaning solutions containing chelating agents with carboxyl acid group (-COOH), such as ethylenediaminetetraacetic acid, citric acid and oxalic acid, were developed for post-poly-Si CMP cleaning. The chelating agent and tetramethylammonium hydroxide (TMAH) were simultaneously added into 2% ammonium hydroxide alkaline solution to promote the removal efficiency on particles and metallic impurities. The effectiveness of various cleaning recipes and their interaction mechanism with the poly-Si surface were studied. We could explain the surface behavior of various cleaning solutions by the different molecular size and charge of chelating agents. Based on the mechanism, the behavior of surface particle and metallic impurity can be realized. The co-existence of TMAH with citric acid or oxalic acid in the alkaline cleaning solutions can significantly enhance the electrical properties of capacitors.
Table S3 from Epigenetic Reprogramming with Antisense Oligonucleotides Enhances the Effectiveness of Androgen Receptor Inhibition in Castration-Resistant Prostate Cancer (2023)

&lt;p&gt;Supplementary Table 3 Primer and sgRNA sequences used in the study.&lt;/p&gt;
ChemInform Abstract: Enzyme‐Catalyzed Interesterification Procedure for the Preparation of Esters of a Chiral Secondary Alcohol in High Enantiomeric Purity. (1990)

Abstract Enzyme‐catalyzed hydrolysis of the racemic acetoxybicyclo(3.2.0)heptene (±)‐(I) yields the (6R)‐alcohol (+)‐(II) with moderate enantiomeric excess.
A preliminary study of the local biomechanical environment of liver tumors in vivo (2019)

Lagrangian strain metrics provide insight into the biomechanical conditions of certain liver tumors in the human body and may provide another perspective for tumor characterization and diagnosis.
Distributed Storage and Analysis of Microarray Data in the Terabyte Range: An Alternative to Bioconductor (2003)

Novel high-throughput technologies such as DNA microarray analyses are allowing biologists to generate sets of data in the terabyte realm. Many of these data will be deposited in the public domain, necessitating a common standard. Currently available database systems are not appropriate for these intentions. In this paper, I will introduce ROOT (http://root.cern.ch), an objectoriented framework that has been developed at CERN for distributed data warehousing and data mining of particle data in the petabyte range. Data are stored as sets of objects in machine-independent files, and specialized methods are used to get direct access to separate attributes of selected data objects. ROOT has been designed in such a way that it can query its databases in parallel on SMP/MPP machines, on clusters of PC’s, or using common GRID services. In order to demonstrate the applicability of ROOT to microarray data, I will present a functional prototype system, called XPS - eXpression Profiling System, which can be considered to be an alternative to the Bioconductor project. The current implementation handles the storage of Aymetrix GeneChip schemes and data, and the pre-processing, normalization and filtering of GeneChip data. Based on this system, I will propose a novel standard for the distributed storage of microarray data. Finally, I will emphasize the similarities between R and ROOT, and show how R could be easily extended to access ROOT from within R.
System for reactivating catalysts (2023)

A method of reactivating a catalyst, such as a solid catalyst or a liquid catalyst is provided. The method comprises providing a catalyst that is at least partially deactivated by fouling agents. The catalyst is contacted with a fluid reactivating agent that is at or above a critical point of the fluid reactivating agent and is of sufficient density to dissolve impurities. The fluid reactivating agent reacts with at least one fouling agent, releasing the at least one fouling agent from the catalyst. The at least one fouling agent becomes dissolved in the fluid reactivating agent and is subsequently separated or removed from the fluid reactivating agent so that the fluid reactivating agent may be reused. A system for reactivating a catalyst is also disclosed.
The FeTouch project (2004)

Ultrasound technologies have been widely used in gynecology and obstetrics. Modern ultrasound systems allow the reconstruction of a 3D model of the subject being scanned. Even though visual interfaces have reached very high standards, the problem of representing a 3D image on a 2D computer screen still exists. Moreover, no physical interaction is possible with such model. The FeTouch system, developed at Siena University in the last two years, partially solves such issues by using stereo visual feedback and haptic devices. While the system can be used with any 3D model obtained from ultrasound scans, its current prime use is to allow mothers to interact with a model of the fetus they are carrying. The system, which is freely available on the project web page, has been tested on twelve cases which have been monitored by doctors at Siena Hospital.
TGF-β Blockade Reduces Mortality and Metabolic Changes in a Validated Murine Model of Pancreatic Cancer Cachexia (2015)

Cancer cachexia is a debilitating condition characterized by a combination of anorexia, muscle wasting, weight loss, and malnutrition. This condition affects an overwhelming majority of patients with pancreatic cancer and is a primary cause of cancer-related death. However, few, if any, effective therapies exist for both treatment and prevention of this syndrome. In order to develop novel therapeutic strategies for pancreatic cancer cachexia, appropriate animal models are necessary. In this study, we developed and validated a syngeneic, metastatic, murine model of pancreatic cancer cachexia. Using our model, we investigated the ability of transforming growth factor beta (TGF-β) blockade to mitigate the metabolic changes associated with cachexia. We found that TGF-β inhibition using the anti-TGF-β antibody 1D11.16.8 significantly improved overall mortality, weight loss, fat mass, lean body mass, bone mineral density, and skeletal muscle proteolysis in mice harboring advanced pancreatic cancer. Other immunotherapeutic strategies we employed were not effective. Collectively, we validated a simplified but useful model of pancreatic cancer cachexia to investigate immunologic treatment strategies. In addition, we showed that TGF-β inhibition can decrease the metabolic changes associated with cancer cachexia and improve overall survival.
Electronic structure of the neutral silicon-vacancy center in diamond (2019)

The neutrally charged silicon vacancy in diamond is a promising system for quantum technologies that combines high-efficiency optical spin initialization with long spin lifetimes (${T}_{2}\ensuremath{\approx}1$ ms at 4 K) and up to 90% of optical emission into its 946-nm zero-phonon line. However, the electronic structure of ${\mathrm{SiV}}^{0}$ is poorly understood, making further exploitation difficult. Performing photoluminescence spectroscopy of ${\mathrm{SiV}}^{0}$ under uniaxial stress, we find the previous excited electronic structure of a single $^{3}A_{1u}$ state is incorrect, and identify instead a coupled $^{3}E_{u}\text{\ensuremath{-}}^{3}A_{2u}$ system, the lower state of which has forbidden optical emission at zero stress and efficiently decreases the total emission of the defect. We propose a solution employing finite strain to define a spin-photon interface scheme using ${\mathrm{SiV}}^{0}$ .
Global shutter pixels with correlated double sampling for CMOS image sensors (2013)

Abstract This article describes the operation and performance of global shutter pixels with correlated double sampling for CMOS image sensors. Correlated double sampling is required to keep the read noise at a level comparable to interline transfer CCDs. A pixel with voltage domain in-pixel sampling of the floating diffusion reset and signal levels is explained and its noise performance is modeled. The saturation level of this pixel is analyzed and parasitic light sensitivity is discussed. The pixel is benchmarked against other global shutter pixels that allow correlated double sampling, based upon charge domain in-pixel storage.
Orthonormal Isotropic Vector Bases (1998)

Abstract Orthonormal bases of isotropic vectors for indefinite square matrices are proposed and solved. A necessary and sufficient condition is that the matrix must have zero trace. A recursive algorithm is presented for computer applications. The isotropic vectors of 3 × 3 matrices are solved explicitly. Deviatoric stresses in continuum mechanics, the existence of isotropic vectors (particularly in screw space), and stiffness synthesis by springs are shown to be related to the isotropic vector problem.