gebhart/patrepeval huggingface dataset:
So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute (2014)

The emerging field of next-generation sequencing (NGS) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine biodiversity are most concentrated. This is particularly true in Southeast Asia. The first Pan-Pacific Advanced Studies Institute (PacASI) entitled "Genomic Applications to Marine Science and Resource Management in Southeast Asia" was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGS in helping address the aforementioned challenges. Here we synthesize discussions held during the PacASI to provide perspectives and guidance to help scientists new to NGS choose among the variety of available advanced genomic methodologies specifically for marine science questions.
Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries (2020)

Core genome analysis suggests that the Salmonella enterica and Citrobacter populations investigated here share a common evolutionary history. Comparative analysis of the core and pan-genomes was able to define the genetic features that distinguish Salmonella from Citrobacter and highlight niche specific adaptations.
<title>Time difference of arrival technology for locating narrowband cellular signals</title> (1996)

Various types of location systems have been proposed for locating cellular telephones. In location systems examined by and field tested by Associated Group, time different of arrival systems have proven to yield the best performance for the signals transmitted by AMPS cellular telephones. The reverse control channel transmissions were identified as the preferred channel to locate due to signal characteristics.
Regulation of genes coding for enzyme constituents of the bacterial phosphotransferase system (1980)

Regulation of the synthesis of the proteins of the phosphoenolpyruvate:sugar phosphotransferase system was systematically studied in wild-type and mutant strains of Salmonella typhimurium and Escherichia coli. The results suggest that enzyme I and HPr as well as the glucose-specific and the mannose-specific enzymes II are synthesized by a mechanism which depends on (i) cyclic adenosine monophosphate and its receptor protein; (ii) extracellular inducer; (iii) the sugar-specific enzyme II complex which recognizes the inducing sugar; and (iv) the general energy-coupling proteins of the phosphotransferase system, enzyme I and HPr.
DeepFIR: Channel-Robust Physical-Layer Deep Learning Through Adaptive Waveform Filtering (2021)

Deep learning can be used to classify waveform characteristics ( <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e.g.</i> , modulation) with accuracy levels that are hardly attainable with traditional techniques. Recent research has demonstrated that one of the most crucial challenges in wireless deep learning is to counteract the channel action, which may significantly alter the waveform features. The problem is further exacerbated by the fact that deep learning algorithms are hardly re-trainable in real time due to their sheer size. This paper proposes <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DeepFIR</i> , a framework to counteract the channel action in wireless deep learning algorithms <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">without retraining the underlying deep learning model</i> . The key intuition is that through the application of a carefully-optimized digital finite input response filter (FIR) at the transmitter’s side, we can apply tiny modifications to the waveform to strengthen its features according to the current channel conditions. We mathematically formulate the <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Waveform Optimization Problem</i> <xref ref-type="disp-formula" rid="deqnWOP-deqnC1" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(WOP)</xref> as the problem of finding the optimum FIR to be used on a waveform to improve the classifier’s accuracy. We also propose a data-driven methodology to train the FIRs directly with dataset inputs. We extensively evaluate <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DeepFIR</i> on an experimental testbed of 20 software-defined radios, as well as on two datasets made up by 500 ADS-B devices and by 500 WiFi devices and a 24-class modulation dataset. Experimental results show that our approach (i) increases the accuracy of the radio fingerprinting models by about 35%, 50% and 58%; (ii) decreases an adversary’s accuracy by about 54% when trying to imitate other device’s fingerprints by using their filters; (iii) achieves 27% improvement over the state of the art on a 100-device dataset; (iv) increases by <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2\times$ </tex-math></inline-formula> the accuracy of the modulation dataset.
Laboratory evaluation of pavement macrotexture durability (2007)

ABSTRACT The aim of this paper is to present a study concerning the evaluation of the durability of the asphalt concrete macrotexture in laboratory. An experimental procedure was developed. This experimental procedure consists in a mechanical test which aims to alter the upper face macrotexture of a cylindrical specimen through the application of a sinusoidal repeated load on its surface. In order to quantify the macrotexture evolution produced we use a laser texture evaluation system. This system allows the scanning of surface specimen before and after mechanical solicitation. In this paper, we first present the materials and the experimental procedure. Then, we expose the various surface indicators analysis and finally we discuss the experimental results.
Parameter extraction of MEMS comb-drive near-resonance equivalent circuit: physically-based technique for a unique solution (2012)

A new extraction approach for MEMS comb-drive equivalent circuit parameters is presented. The proposed method eliminates the need for fitting and optimization by direct extraction from the measured data and, thus, avoids the nonuniqueness problem associated with fitting algorithms. A silicon-on-insulator-based MEMS comb-drive actuator is designed, fabricated, and measured, and its equivalent circuit is obtained by the proposed procedure. Analytical estimation for the uncertainty in the extracted values due to the discrete nature of the measurement frequency resolution is carried out. Uncertainty in the extracted values of the equivalent motional parameters is well below 0.6% when a 0.1-Hz frequency resolution is used. The method has been used to extract the resonator quality factor at both atmospheric and vacuum operations and can be extended to other types of resonators.
Performance of Bidirectional LiFi over Plastic Optical Fiber (POF) (2020)

In this paper, we report on a bidirectional LiFi link integrated with a plastic optical fiber (POF) acting as fronthaul to make the system fully robust against electromagnetic interference in aircraft, industrial wireless, and offices. We have implemented the POF link using two specifically developed printed circuit boards interfacing directly with the DSP and the LiFi frontends. The fronthaul transports analog LiFi baseband signals transparently over the POF in a bandwidth of 200 MHz. The compound POF and LiFi link has been tested in several configurations and achieved unprecedented throughputs of 725 Mbit/s and 901 Mbit/s in forward and reverse link direction, respectively.
CD56negCD16+ NK cells are mature NK cells generated from CD56+CD16+ NK cells during HIV-1 infection (P4438) (2013)

Abstract A subset of CD3negCD56negCD16+ Natural Killer (NK) cells is highly expanded during chronic HIV-1 infection, and the role of this subset in HIV-1 pathogenesis remains unclear. The lack of NK cell lineage-specific markers has complicated the study of minor NK cell subpopulations. Using CD7 as an additional NK cell marker, we found that CD3negCD56negCD16+ cells are a mixed population of CD7+ NK cells and CD7neg myeloid cells. CD7+CD56negCD16+ NK cells are significantly expanded in HIV-1 infection. CD7+CD56negCD16+ NK cells are mature and express KIRs, NKG2A, NKG2C, and natural cytotoxicity receptors similar to CD7+CD56+CD16+ cells. CD7+CD56neg NK cells in healthy donors produced minimal IFNg following K562 target cell or IL-12 plus IL-18 stimulation; however, they did degranulate in response to K562 cells similar to CD7+CD56+ NK cells. HIV-1 infection resulted in reduced IFNg secretion following K562 or cytokine stimulation by both NK cell subsets compared to healthy donors. Decreased granzyme B and perforin expression and increased expression of CD107a in the absence of stimulation, particularly in HIV-1-infected subjects, suggests that CD7+CD56negCD16+ NK cells may have recently engaged target cells. CD7+CD56negCD16+ NK cells have increased expression of the aging-related cyclin-dependent kinase inhibitors p16/INK4a and p21/Waf1. Taken together, CD7+CD56negCD16+ NK cells appear to be mature NK cells generated from chronic target engagement.
Grasp invariance (2012)

This paper introduces a principle to guide the design of finger form: invariance of contact geometry over some continuum of varying shape and/or pose of the grasped object in the plane. Specific applications of this principle include scale-invariant and pose-invariant grasps. Under specific conditions, the principle gives rise to spiral shaped fingers, including logarithmic spirals and straight lines as special cases. The paper presents a general technique to solve for finger form, given a continuum of shape or pose variation and a property to be held invariant. We apply the technique to derive scale-invariant and pose-invariant grasps for disks, and we also explore the principle’s application to many common devices from jar wrenches to rock-climbing cams.
Advanced Imaging and Direct Targeting of the Motor Thalamus and Dentato-Rubro-Thalamic Tract for Tremor: A Systematic Review (2020)

Direct targeting methods for stereotactic neurosurgery in the treatment of essential tremor have been the subject of active research over the past decade but have not yet been systematically reviewed. We present a clinically oriented topic review based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses Group guidelines. Our focus is studies using advanced magnetic resonance imaging (MRI) techniques (ultrahigh-field structural MRI, diffusion-weighted imaging, diffusion-tensor tractography, and functional MRI) for patient specific, in vivo identification of the ventral intermediate nucleus and the dentato-rubro-thalamic tract.
Cellular and genetic restrictions in the immunoregulatory activity of alpha-fetoprotein. II. Alpha-fetoprotein-induced suppression of cytotoxic T lymphocyte development. (1978)

Alpha-fetoprotein (AFP), a major component of fetal and newborn sera, was shown to exert significant immunosuppressive activity on the in vitro generation of cytotoxic T lymphocytes (CTLs). This suppression proved independent of the suppressibility of the mixed leukocyte culture activation phase, since strain combinations whose proliferative responses were refractive to AFP-induced suppression also failed to develop demonstrable CTLs in the presence of AFP. Several strain combinations were also found in which normal generation of CTLs occurred in cultures containing AFP. This refractive nature correlated with the presence of nonsuppressible lymphocyte-stimulating alloantigenic systems on the stimulating cell population. These data provide the basis for proposing several possible mechanisms for AFP-induced suppression of T-cell-mediated cytotoxicity, as well as suggesting that the primary target of this suppression is the proliferating helper T cell precommited to respond towards the major histocompatibility complex-associated lymphocyte-activating determinants.
Microgeographic Proteomic Networks of the Human Colonic Mucosa and Their Association With Inflammatory Bowel Disease (2016)

These findings suggest that the mucosal surface is a microgeographic mosaic of functional networks reflecting the local mucosal ecology, whose compositional differences in disease and healthy samples may provide a unique readout of physiologic and pathologic mucosal states.
Mapping of a Mycoplasma-Neutralizing Epitope on the Mycoplasmal p37 Protein (2016)

Many studies have shown that the mycoplasmal membrane protein p37 enhances cancer cell migration, invasion, and metastasis. Previously, we generated 6 monoclonal antibodies (MAbs) against the mycoplasmal protein p37 and showed the presence of mycoplasma-infected circulating tumor cells in the blood of hepatocellular carcinoma patients by using CA27, one of the six MAbs. When mycoplasmas were incubated with cancer cells in the presence of CA27, mycoplasma infection was completely inhibited, suggesting that CA27 is a neutralizing antibody inhibiting mycoplasma infection. To examine the neutralizing epitope of CA27, we generated a series of glutathione S-transferase (GST)-fused p37 deletion mutant proteins in which p37 was partly deleted. To express p37-coding sequences in E.coli, mycoplasmal TGA codons were substituted with TGG in the p37 deletion mutant genes. GST-fused p37 deletion mutant proteins were then screened to identify the epitope targeted by CA27. Western blots showed that CA27 bound to the residues 216-246 on the middle part of the p37 protein while it did not bind to the residues 183-219 and 216-240. Fine mapping showed that CA27 was able to bind to the residues 226-246, but its binding activity was relatively weakened as compared to that to the residues 216-246, suggesting that the residues 226-246 is essential for optimal binding activity of CA27. Interestingly, the treatment of the purified GST-tagged epitopes with urea showed that CA27 binding to the epitope was sodium dodecyl sulfate-resistant but urea-sensitive. The same 226-246 residues were also recognized by two other anti-p37 MAbs, suggesting that the epitope is immunodominant. The identification of the novel neutralizing epitope may provide new insight into the interaction between the p37 protein and host receptors.
Investigation of metal–dithiolate fold angle effects: Implications for molybdenum and tungsten enzymes (2003)

Gas-phase photoelectron spectroscopy and density functional theory have been used to investigate the interactions between the sulfur pi-orbitals of arene dithiolates and high-valent transition metals as minimum molecular models of the active site features of pyranopterin MoW enzymes. The compounds (Tp*)MoO(bdt) (compound 1), Cp(2)Mo(bdt) (compound 2), and Cp(2)Ti(bdt) (compound 3) [where Tp* is hydrotris(3,5-dimethyl-1-pyrazolyl)borate, bdt is 1,2-benzenedithiolate, and Cp is eta(5)- cyclopentadienyl] provide access to three different electronic configurations of the metal, formally d(1), d(2), and d(0), respectively. The gas-phase photoelectron spectra show that ionizations from occupied metal and sulfur based valence orbitals are more clearly observed in compounds 2 and 3 than in compound 1. The observed ionization energies and characters compare very well with those calculated by density functional theory. A "dithiolate-folding-effect" involving an interaction of the metal in-plane and sulfur-pi orbitals is proposed to be a factor in the electron transfer reactions that regenerate the active sites of molybdenum and tungsten enzymes.
Construction of a Hexameric Hemoprotein Sheet and Direct Observation of Dynamic Processes of Its Formation (2019)

A two-dimensional sheet assembly of a hexameric hemoprotein was constructed. A single cysteine residue was introduced onto each subunit surface in the hexameric hemoprotein and modified with a male...
Automated ‘pain drawing’ analysis by computer-controlled, patient-interactive neurological stimulation system (1992)

We have developed a new method for the collection and analysis of pain drawings, as part of a computer-controlled, patient-interactive system for use with implanted neurological stimulators. The system has been tested in 44 patients with permanently implanted spinal cord stimulators for the relief of chronic, intractable pain. Patients interact directly with the system, using a graphics tablet, to enter pain drawings and corresponding outlines of their perceptions of stimulation paresthesias, for different stimulating pulse parameters and electrode geometries. Image analysis software has been developed to examine these data quantitatively. This precludes the inter-rater inconsistencies reported for manual pain drawing scoring techniques. A highly significant correlation has been observed between patients' analog ratings of the overlap of pain by paresthesias and the results of our automated analysis of graphic data. This in turn has been found to correlate with clinical observations of pain relief. The contemporary implantable stimulation devices supported by our system permit non-invasive selection of stimulating anodes and cathodes from a linear array of 4 electrodes. The 50 possible electrode combinations have certain geometric features, which we have entered into a multivariate statistical analysis, to determine their relationship with the overlap of pain by paresthesias. One particular configuration (cathode(s) flanked by anode(s) above and below) is significantly better, by this measure, than all the alternatives. This is consistent with prior clinical observations that this configuration is favored by patients whose systems have been adjusted by conventional, manual methods. Pain drawing' entry and analysis by a computerized, patient-interactive system has been useful in this specialized setting and may have broader applications.
Fluoroscopic navigation system for hip surface replacement (2007)

Metal-on-metal hip resurfacing arthroplasties represent an alternative to total hip arthroplasties for young and active patients, enabling the preservation of intact femoral bone and therefore improving the prognosis for future hip joint replacements. Follow-up studies have shown that the main reasons for early implant failure are mal-orientation of the implant stem in relation to the femoral neck axis, and notching of the femoral neck during femoral head preparation, as well as by exposed cancellous bone after implantation. A computer-assisted planning and navigation system for the implantation of femoral hip resurfacing implants has been developed which supports the surgeon during intraoperative fluoroscopy-based planning and navigation of implant positioning. This paper presents the results of a cadaver study performed to evaluate the system's functionality and accuracy.
Supplementary Figure 4 from Prostate Cancer Progression Correlates with Increased Humoral Immune Response to a Human Endogenous Retrovirus GAG Protein (2023)

&lt;p&gt;- PDF file 418K, Characterization of TI-35 mAb by subcellular colocalization of staining with GAG-HERV-K expression and by transfection. A-B, Confocal images of HeLa cells transfected with GAG-HERV-K_GFP (A) or GFP only (B) and stained with TI-35. Blue represents DAPI nuclear staining, green represents GFP, and purple represents TI-35 staining. Colocalization is observed in the merged data as white, in areas indicated by arrows. Axes in the corner of each quadrant show size/magnification information. C-D, TI-35 immunostaining with formalin-fixed Sf9 insect cells infected with GAG-HERV-K-recombinant baculovirus (C) or control baculovirus (D). Original magnification (objective) was 4x, and insets show zoomed area at 20x&lt;/p&gt;
Differentiation Inductions Altered Telomere Length and Telomerase Activity in Human Dental PulpDerived Mesenchymal Stem Cell (2019)

Hyeon-Jeong Lee, Ryoung-Hoon Jeon, Byung-Joon Park, Si-Jung Jang, Sung-Lim Lee, Gyu-Jin Rho, Seung-Joon Kim and Won-Jae Lee. Journal of Animal Reproduction and Biotechnology 2019;34:93-9. https://doi.org/10.12750/JARB.34.2.93
EXPANDING THE ROLE OF COMMUNITY PHARMACY: AN EVALUATION OF GENERIC DRUG DISCOUNT PROGRAMS, PHARMACY BASED IMMUNIZATION SERVICES AND CONVENIENT CARE CLINICS (2012)

We evaluated the clinical and economic impact of generic drug discount programs (GDDPs), pharmacy based immunization services and convenient care clinics (CCCs) based upon existing literature, reviewing original research and case study reports using library databases, primarily MEDLINE and EBSCOHost. Keywords used included “generic discount list,” “four dollar generic,” “pharmacy immunization,” “flu shot,” “pharmacist immunizer,” “convenient care clinic,” “retail health clinic,” and “minute clinic.” We then added other terms such as “clinical impact,” “cost-effectiveness,” “outcomes,” and “perceptions.” While all 3 programs have the potential to clinically benefit patients and provide some level of cost-effectiveness, there are also concerns that need to be addressed. Some concerns include: a) GDDPs have the potential to cause fragmentation of care owing to patients going to other pharmacies in search of lower prices and prescription claims data not being captured by patients’ pharmacy benefit managers, b) GDDPs may be less cost effective in pharmacies with less purchasing power compared to larger chains, c) pharmacy based immunization services still face legal and social barriers that prevent pharmacists from being recognized as legitimate vaccine administrators, d) some insurance carriers still don’t pay for pharmacist-administered vaccinations, e) CCCs may not currently be located in areas that could best benefit from their services, f) CCCs may disrupt a patient’s continuity of care with their primary care physicians, and g) CCCs may hinder the efforts of pharmacists to expand their own professional roles by lessening the need for them to do so. Expanding the roles of community pharmacies has the potential to improve patient care by increasing patients' access to healthcare services. While strong evidence exists to support pharmacist-delivered immunizations, less is known regarding GDDPs and CCCs. More studies are required to assess the clinical and economic questions raised regarding these types of programs.
Direct intracellular injections for studying human myometrial gap junctions prior to labor (1994)

Direct intracellular microinjection of a fluorescent dye (Lucifer Yellow) was performed on ex-situ muscle strips from term pregnant women not in labor. The aim was to characterize the intracellular distribution of LY to obtain criteria for an intracellular injection in whole mounts and ultimately to study the gap junctional communication between myometrial cells in those tissues. Fifteen injections performed on biopsies from ten cases showed a well-bordered fusiform shape and were considered to be intracellular. The intercellular spread of the dye into an adjacent cell was observed in three injections (three cases). The average cell dimension was 284 +/- 95 microns for length and 5 +/- 1.5 microns for width (n = 17). The intracellular injection was confirmed by light microscopy of cross sections. It is concluded that limited coupling exists between myometrial cells of women prior to labor.