gebhart/patrepeval huggingface dataset:
Representation is Everything: Towards Efficient and Adaptable Similarity Measures for Biological Data (2006)

Distance function computation is an important operation in biological data mining. This is because the notion of similarity is often required as a key subroutine in many data mining algorithms such as clustering, search or indexing. Furthermore, since such applications typically require repeated distance function computation, it is desirable to perform this task as efficiently as possible. A wide variety of alignment functions have been designed in the literature in order to determine similarity between biological strings. Typically, most of these methods such as the edit distance or the Smith-Waterman algorithm rely on either a local or global form of alignment between the two string representations of the biological data. Yet, many of these methods suffer from a variety of drawbacks both in terms of effectiveness and efficiency in measuring similarity. In this paper, we examine the key qualitative issues in measurement of similarity among distance functions, and question the fundamental assumptions in using alignment measures over string representations of the biological data. We argue that the alignment approach is rigid and brittle, ignores several relevant compositional characteristics of the strings, is not easily trainable from examples, and is inherently resistant to an efficient data mining process from a representational point of view. We propose a fundamental overhaul in the methods for similarity computation of biological data by changing the underlying representation of the data. Our proposed methodology (PROSAC) uses PRObabilistic SAmpling for similarity Computations, and results in a new representation of the strings at a higher level of abstraction; yet the abstraction process has the effect of removing the noise in the distance measurements of precise alignment techniques. In addition, some forms of string representation in the PROSAC approach map to well known representational and distance computation methods in the data mining field, and therefore existing data mining software can be used directly and efficiently on the new representation. We also show that the approach is amenable to the use of supervision for parametric determination of efficient distance functions for particular tasks in biological analysis.
Curcumin-Zein Nanospheres Improve Liver Targeting and Antifibrotic Activity of Curcumin in Carbon Tetrachloride-Induced Mice Liver Fibrosis (2016)

Liver fibrosis is a major health problem that has no satisfactory medication. Curcumin, (CUR) although known for its antifibrotic activity, has limited medicinal use owing to its poor oral pharmacokinetic properties and targeting efficiency. The current study aimed at exploring the ability of zein (ZN) nanospheres to improve the liver targeting and antifibrotic activity of CUR in a mouse model of carbon tetrachloride (CCl4)-induced liver fibrosis. Four different formulae of ZN-loaded CUR were prepared and examined in terms of particle size, zeta potential, encapsulation efficiency, and in vitro permeation. The formula containing a CUR to ZN ratio of 1:3 showed optimum nanosphere properties and was subjected to further investigations. Under a scanning electron microscope, the selected formula showed spherical particles with uniform size distribution. In normal mice, the selected formula exhibited improved bioavailability and liver targeting efficiency compared to raw CUR. The nanosphere preparation also offered significant protection against CCl4-induced liver function deterioration, histopathological changes, and oxidative stress in mice. Compared to raw CUR, CUR-ZN was significantly more effective in attenuating the rise in hepatic gene expression of collagen-1, tissue inhibitor of metalloproteinase-2, and transforming growth factor beta, as well as the downregulation of matrix metalloproteinase-2 expression. Masson's trichrome staining confirmed the higher antifibrotic activity of the nanospheres that ameliorated the rise in hepatic hydroxyproline content and collagen-1-immunopositive areas in mice liver sections. In conclusion, CUR-ZN nanospheres demonstrated improved liver targeting efficiency and antifibrotic activity in comparison to raw CUR in CCl4-induced liver fibrosis in mice.
Ubiquitin-conjugating enzyme Ubc13 is a critical component of TNF receptor-associated factor (TRAF)-mediated inflammatory responses (2007)

Ubc13 is a ubiquitin-conjugating enzyme responsible for noncanonical ubiquitination of TNF receptor-associated factor (TRAF)-family adapter proteins involved in Toll-like receptor and TNF-family cytokine receptor signaling, which are regulators of innate immunity. Gene ablation was used to study the function of Ubc13 in mice. Whereas homozygous ubc13 gene disruption resulted in embryonic lethality, heterozygous ubc13(+/-) mice appeared normal, without alterations in immune cell populations. Haploinsufficient ubc13(+/-) mice were resistant to lipopolysaccharide-induced lethality, and demonstrated reduced in vivo ubiquitination of TRAF6. Macrophages and splenocytes isolated from ubc13(+/-) mice exhibited reduced lipopolysaccharide-inducible cytokine secretion and impaired activation of TRAF-dependent signal transduction pathways (NF-kappaB, JNK, and p38 MAPK). These findings document a critical role for Ubc13 in inflammatory responses and suggest that agents reducing Ubc13 activity could have therapeutic utility.
Supplementary Table 3 from TYK2–STAT1–BCL2 Pathway Dependence in T-cell Acute Lymphoblastic Leukemia (2023)

&lt;p&gt;XLSX file - 30K, Targeting sequences for shRNAs.&lt;/p&gt;
13C n.m.r. in organic solids: limits to spectral resolution and to determination of molecular motion (1981)

Abstract The history of high-resolution n.m.r. in solids has been, inter alia, a quest for narrow spectral lines. Yet, with few exceptions, solid state resonances have not been sharpened to the degree of liquid resonances. To aid in the appraisal of the status of n.m.r. in solids, we identify and summarize, for the particular case of 13C n.m.r. in organic solids, those effects that can degrade resolution. Some of these mechanisms are under the experimenter’s control; for example, certain are exacerbated at high magnetic field. Others, however, represent fundamental limitations imposed by the specimen and are valid reflections of the complexity of a solid as contrasted to a liquid. In solids, magnetic dipolar spin-spin couplings can not only degrade resolution but also complicate, hopelessly in some cases, the determination of spin-lattice relaxation rates from which one seeks information about molecular motions. The consequences of this competition between spin-spin and spin-lattice effects are examined, as well as criteria and strategies to isolate the motional contributions to relaxation rates.
Compressed Sensing for Feedback Generation in OFDM Based LiFi Systems (2023)

In this paper, we evaluate the effectiveness of compressed-sensing-based channel estimation in LiFi orthogonal frequency-division multiplex (OFDM) systems with multiple-input multiple-output (MIMO). The sparseness of LiFi channels suggests that it is beneficial to utilize compressed sensing which has been investigated also for radio communications. In this paper, we formulate the mathematical problem of compressed-sensing for feedback generation in OFDM-based LiFi systems. We use well-known algorithms for both, sparse pilot design and sparse recovery and apply them to LiFi OFDM channels. We evaluate the effectiveness of these algorithms by measuring the achievable mean squared error (MSE) and vary the total numbers of subcarriers as well as the number of pilot subcarriers.
EXPRESSION OF CYCLOOXYGENASE‐2 (COX‐2) IN PRE‐MALIGNANT GASTRIC LESIONS BEFORE AND AFTER H. PYLORI ERADICATION (2000)

Objective COX‐2 is frequently expressed in gastric cancer, which may play a active role in carcinogenesis, tumor invasion and metastatis. To evaluate the distribution and expression of COX‐2 in various stages of gastric carcinogenesis and monitor the changes of COX‐2 in intestinal metaplasia (IM) after H. pylori eradication. Methods Gastric biopsies were selected from a group of H. pylori infected patients with various histological diagnosis of chronic active gastritis (CAG, n=40), gastric atrophy (GA, n=20), IM (n=51) and adenocarcinoma (CA, n=25). Non‐infected (n=40) were included as control. Expression of COX‐2 was examined by immunohistochemistry and scored in a semiquantitative manner: 0 = negative , 1 = &lt;5% cells with positive staining, 2 = 5‐30%, 3 = 30‐60% and 4 = &gt;60%. Cellular localization of COX‐2 was further confirmed by in‐situ hybridization of COX‐2 mRNA using an anti‐sense RNA probe. In subgroup of patients with IM, the experissions of COX‐2 one‐year after successful H. Pylori eradication was compared with pre‐treatment level. Results COX‐2 expressions were detected in all H.Pylori‐infected patients irrespective of histological diagnosis. In Contrast, only 14 (35%) H. Pylori‐negative control expressed weak COX‐2 expression (median score 0 vs 2; P&lt;0.0001). However, there was no difference in the intensity of COX‐2 expression between CAG, GA, IM and CA patients. Among the 17 IM patients who had received successful H. Pylori eradication therapy, there was a modest reduction of COX‐2 expressions in both epithelial (P=0.049) and stromal cells (P=0.001) at one‐year. However, there was no significant change in the severity of IM, not any correlation between changes in IM and COX‐2 expression, at one‐year follow‐up. Conclusion Both premalignant and malignant gastric lesions show strong COX‐2 expression. Although successful eradication of H. pylori reduces the level of COX‐2 expression, there is no association with regression of IM at one year.
Technical note: Creating a four‐dimensional model of the liver using finite element analysis (2002)

Finite element analysis and two liver CT scans were used to construct a four-dimensional (4D) model of the liver during breathing. A linear elastic, small deformation mechanical model was applied to one patient to obtain intermediate organ position and shape between exhale and inhale. Known transformations between anatomically defined subsections of the exhale and inhale liver surfaces were applied as constraints to the exhale CT liver model. Intermediate states were then calculated and time weighted to determine a 4D model of the liver as it deforms during the breathing cycle. This model can be used to calculate a more accurate dose distribution during radiotherapy.
Ocean acoustic tomography: estimating the acoustic travel time with phase (1989)

Continuous acoustic transmission (133 Hz, 60-ms resolution) between a bottom-mounted source near Oahu, Hawaii, and a bottom-mounted receiver at 4000-km range near the coast of northern California was recorded to learn how to measure precisely the travel time so that basin-scale fluctuations in the Pacific can be detected. Daily incoherent averages of some of the multipaths exhibited stability during this period. The standard deviation of the travel time of the resolved peaks in the daily incoherent averages is about 30 ms. An acoustic method, based on cross-correlation, is derived to estimate the change in the average acoustic phase (travel time) to a precision of about 0.018 cycles (135 mu s) every 2 min. Travel-time estimates based on the cross-correlator reduce the aberrations due to internal waves by about 19 dB in comparison with CW transmissions. The new travel-time estimator is applied to the measurements to examine some of the fluctuations of the Pacific.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improving Sorbents for Glycerol Capture in Biodiesel Refinement (2017)

Biodiesel is produced by transesterification of animal fat, vegetable oil, or waste cooking oil with alcohol. After production costs, the economic viability of biodiesel is dependent on what steps are necessary to remove impurities following synthesis and the effectiveness of quality control analysis. Solid-phase extraction offers a potentially advantageous approach in biodiesel processing applications. Nanoporous scaffolds were investigated for adsorption of glycerol, a side product of biodiesel synthesis that is detrimental to engine combustion when present. Materials were synthesized with varying pore wall composition, including ethane and diethylbenzene bridging groups, and sulfonated to promote hydrogen bonding interactions with glycerol. Materials bearing sulfonate groups throughout the scaffold walls as well as those post-synthetically grafted onto the surfaces show notably superior performance for uptake of glycerol. The sorbents are effective when used in biodiesel mixtures, removing greater than 90% of glycerol from a biodiesel preparation.
Progress in self-quenching InP-based single photon detectors (2010)

The operation of InP-based single photon avalanche diodes (SPADs) in Geiger mode provides great utility for the detection of single photons at near-infrared wavelengths between 1.0 and 1.6 &#956;m. However, SPADs have performance limitations with respect to photon counting rate and the absence of photon number resolution that, at the most fundamental level, can be traced back to the positive feedback inherent in the impact ionization-driven avalanche process. In this paper, we describe the inclusion of negative feedback with best-in-class InP-based single photon avalanche diode (SPAD) structures to form negative feedback avalanche diodes (NFADs) in which many of the present limitations of SPAD operation can be overcome. The use of thin film resistors as monolithic passive negative feedback elements ensures rapid self-quenching with very low parasitic effects. We demonstrate a qualitative difference in the performance of NFADs in the two regimes of small and large negative feedback. With small feedback, we have studied the behavior of the persistent current prior to quenching, for which we have found oscillatory behavior as well as an exponentially distributed duration. For large feedback, we find rapid quenching, accompanied by evidence for a partial discharge of the detector capacitance, leading to charge flows as low as ~3 ×10<sup>5</sup> carriers associated with each avalanche event.
Chain Length Effects on Frictional Behavior of Confined Ultrathin Films of Linear Alkanes under Shear (1998)

Molecular dynamics simulations have been performed to study the effect of molecular chain length on frictional behavior of confined thin liquid films under shear. One of the walls confining the films, composed of linear alkanes (chain length 6−80), was moved at a constant velocity for two different pressures. The results indicate that there are distinct differences in frictional behavior under fast sliding velocity between low and high pressures. Under high pressure, interfacial slip appears between the moving wall, base, and the film, and shear stress doe not depend on the chain length. On the other hand, for low pressure, interlayer slips within the film appear in longer chains and shear stress depends on the chain length. In the interfacial and interlayer slip regions, more heat generated by friction is observed. Also, the interfacial shear stress is caused by the slider, interlayer shear stress is caused by interwined and locked layers, and both these stresses have maximum values. When the maximum interfacial shear stress is larger than the maximum interlayer shear stress, interlayer slips occur and in the reverse, interfacial slip occurs. When both maximum shear stresses are larger than the required shear stress for the film to have a uniform shear rate, there is no slip.
Study on Transient Liquid Insert Metal Diffusion Bonding of Ni-base Superalloys(Part 6). Newly Development in Transient Liquid Insert Metal Diffusion Bonding Using Alloying Powder. (1991)

This study developed the new Transient Liquid Insert Metal Diffusion Bonding (TLIM-bonding) technique using alloying powder whose chemical compositions were similar to those of base metal. The base metals used were commercial Ni-base superalloys such as MM007, MarM247 and Inconel 713C alloys. They were bonded with both a Ni-15%Cr-4%B amorphous insert metal and IN100 alloying powder sheet with the thickness of about 250 μm.In the case of a MM007 alloy, the times required for completion of isothermal solidification and sequent homogenizing process were about 0.6 ks and 86.4 ks at 1423 K, respectively using this technique even with the bonding clearance of about 100 μm. The former time was about 1/80 and the latter time was about 1/30 compare to the times obtained by a conventional TLIM bonding. The short period during homogenizing process may be due to element diffusion from alloying powder to base metal by three-dimensional diffusion process.The tensile strength of MM007, MarM247 and Inconel 713C joints at 1255 K were almost equal to those of each base metal, respectively.From the experimental results, it should be useful to insert alloying powder to a wide bonding clearance joint during TLIM-bonding in fabrication
A QRD-Based Array Lattice Form for H<sup>∞</sup> Adaptive Filtering (2021)

In this research note, we present an array lattice algorithm for H∞ adaptive filtering, in which pre-arrays are transformed into post-arrays by J-unitary transformations regarding an indefinite signature matrix J. The array form is derived by factorization with respect to an indefinite Hermitian matrix, which functionally corresponds to the so-called conversion factor in recursive least-squares algorithms. The numerical stability of the array lattice form in finite-precision arithmetic is verified by simulation in comparison with the standard H∞ filter implementation.
Phase locked loop robustness improvement using non integer order loop filter (2006)

This paper presents how noninteger order filters can be used in phase locked loop (PLL) based frequency synthesizers in order to increase their stability robustness. Application to a 192MHz PLL involved in a 3.6GHz multimode double loop frequency synthesizer is described
Abstract 529: Assessing Hemostasis and Platelet Function Using a Microfluidic Device Lined with Fixed Human Endothelium (2016)

Mutual signaling between endothelium and platelets is widely recognized as critical for regulation of hemostasis and thrombotic disorders associated with various diseases, such as, arteriosclerosis, sepsis, and diabetes. Yet no reliable and practical assays exist that can measure the effects of cross-talk between platelets and inflamed vessel walls in the presence of physiological shear. Flow chambers have been applied previously to study basic science, but they have not been used in practical settings due to the difficulty in maintaining living cells in devices. Specifically, because it is extremely difficult to maintain living cell cultures for extended times, it would be impossible to maintain the robustness of these assays. Here, we describe a microfluidic device lined by a chemically fixed human endothelium that retains its ability to support thrombus formation in the presence of blood flow for multiple days under standard storage conditions. We coat the inner surface of a rectangular device with collagen and then culture with endothelial cells on all four walls in order to create a vascular tube. Under activation by increasing doses of TNF-α followed by fixation, the device continues to exhibit multiple proinflammatory and adhesion molecules. Correspondingly, a dose-dependent increase in platelet adhesion to the endothelial layer is also observed. Importantly, we do not observe any significant difference in platelet adhesion between living and fixed endothelium. Furthermore, the morphology of thrombi appears similar to that of thrombi that form on living endothelium of a laser-injured mouse in vivo . To establish clinical utility, we also perfused whole blood of patients taking antiplatelet drugs, and found that these subjects showed a significant reduction in platelet adhesion in our devices. In contrast, conventional aggregometry analysis was very time consuming and tedious. Also, on a collagen-coated flow chamber we found no significant difference in platelet coverage between normal controls and patients. Taken together, this study confirms that this microdevice-incorporating fixed endothelium, whole blood and shear stress-can be used as a global hemostasis assay in research as well as many practical and clinical settings.
364: Effect on interruption of CXCR4-CXCL12 and VLA4-VCAM1 axes on mobilization and sensitization of leukemia cells and normal stem cells to chemotherapy (2007)

Hematopoietic stem cells (HSC) interact with stromal cells, osteoblasts and matrix proteins in the hematopoietic niche. This interaction plays an important role in HSC trafficking, proliferation and differentiation. Significant data support the roles of both the SDF-1/CXCR4 and the VCAM1-VLA-4 axes in stem cell homing and mobilization. Little is known regarding the impact of these ligand-receptor pairs in leukemia cell trafficking. We hypothesize that both CXCR4+VLA-4 play important roles in leukemia cell trafficking while also transmitting protective signals enhancing survival and resistance to chemotherapy and that their blockade may enhance the sensitivity of AML to chemotherapy. To evaluate this we developed a model of human APL in which the PML-RARα is “knocked-into” the mouse cathepsin G locus allowing for expression in the promyelocyte compartment. APL tumors generated from these CGPR/+mice were transduced with retroviral contructs containing the Click Beetle Red/eGFP optical imaging reporter gene for tracking APL cells using bioluminescence imaging (BLI). Unlike other AML cell lines tested these APL cells rapidly migrated to the BM (femurs and spine) by day +4 followed by egress to the spleen (+11) then to the peripheral blood and death (+18-22). The administration of AMD3100, a CXCR4 antagonist, induced a rapid mobilization of normal HSC and leukemia cells from the BM into peripheral blood (PB). The addition of AMD3100 1 hour before and 3 hours after either ara-C or daunorubicin on day +11 resulted in significant improvement in overall survival and decrease in total photon emission compared to those mice treated with chemotherapy alone. We have extended these studies using an inhibitor of VLA-4 (AMD15057) and have shown that this molecule directly mobilizes HSC and APL cells from the BM into the peripheral blood within minutes and when administered with AMD3100 has a synergistic effect on both HSC and APL mobilization. Current studies are aimed at looking at in vitro and in vivo effects of blocking CXCR4 and VLA-4 axes on normal HSC and leukemia cell mobilization and what effects these events might have on the sensitivity of normal and leukemic stem cells to chemotherapy and other genotoxic stresses.
Binocular combination of stimulus orientation (2016)

When two sine waves that differ slightly in orientation are presented to the two eyes separately, a single cyclopean sine wave is perceived. However, it is unclear how the brain calculates its orientation. Here, we used a signal detection rating method to estimate the perceived orientation when the two eyes were presented with Gabor patches that differed in both orientation and contrast. We found a nearly linear combination of orientation when both targets had the same contrast. However, the binocular percept shifted away from the linear prediction towards the orientation with the higher contrast, depending on both the base contrast and the contrast ratio. We found that stimuli that differ slightly in orientation are combined into a single percept, similarly for monocular and binocular presentation, with a bias that depends on the interocular contrast ratio. Our results are well fitted by gain-control models, and are consistent with a previous study that favoured the DSKL model that successfully predicts binocular phase and contrast combination and binocular contrast discrimination. In this model, the departures from linearity may be explained on the basis of mutual suppression and mutual enhancement, both of which are stronger under dichoptic than monocular conditions.