gebhart/patrepeval huggingface dataset:
Structural and functional characterization of a bifunctional GH30-7 xylanase B from the filamentous fungus Talaromyces cellulolyticus (2019)

Glucuronoxylanases are endo-xylanases and members of the glycoside hydrolase family 30 subfamilies 7 (GH30-7) and 8 (GH30-8). Unlike for the well-studied GH30-8 enzymes, the structural and functional characteristics of GH30-7 enzymes remain poorly understood. Here, we report the catalytic properties and three-dimensional structure of GH30-7 xylanase B (Xyn30B) identified from the cellulolytic fungus <i>Talaromyces cellulolyticus</i> Xyn30B efficiently degraded glucuronoxylan to acidic xylooligosaccharides (XOSs), including an α-1,2-linked 4-<i>O</i>-methyl-d-glucuronosyl substituent (MeGlcA). Rapid analysis with negative-mode electrospray-ionization multistage MS (ESI(-)-MS <i><sup>n</sup></i> ) revealed that the structures of the acidic XOS products are the same as those of the hydrolysates (MeGlcA<sup>2</sup>Xyl <i><sub>n</sub></i> , <i>n</i> > 2) obtained with typical glucuronoxylanases. Acidic XOS products were further degraded by Xyn30B, releasing first xylobiose and then xylotetraose and xylohexaose as transglycosylation products. This hydrolase reaction was unique to Xyn30B, and the substrate was cleaved at the xylobiose unit from its nonreducing end, indicating that Xyn30B is a bifunctional enzyme possessing both endo-glucuronoxylanase and exo-xylobiohydrolase activities. The crystal structure of Xyn30B was determined as the first structure of a GH30-7 xylanase at 2.25 Å resolution, revealing that Xyn30B is composed of a pseudo-(α/β)<sub>8</sub>-catalytic domain, lacking an α6 helix, and a small β-rich domain. This structure and site-directed mutagenesis clarified that Arg<sup>46</sup>, conserved in GH30-7 glucuronoxylanases, is a critical residue for MeGlcA appendage-dependent xylan degradation. The structural comparison between Xyn30B and the GH30-8 enzymes suggests that Asn<sup>93</sup> in the β2-α2 loop is involved in xylobiohydrolase activity. In summary, our findings indicate that Xyn30B is a bifunctional endo- and exo-xylanase.
Quantitative analysis of phytoestrogens in kudzu‐root, soy and spiked serum samples by high‐pressure liquid chromatography (2004)

A sensitive and reliable HPLC method that allows simultaneous quantification of phytoestrogens extracted from kudzu-root and soy preparations, and serum samples has been developed. Kudzu-root and soy preparations were mixed with 5 microg flavone and 15 microg rutin (internal standards) and the phytoestrogens were extracted by using solid-phase (C18) extraction cartridges. Blank or spiked serum samples were extracted by using either C18 cartridges or trichloroacetic acid-methanol extraction. The extracts were analyzed by the HPLC equipped with a reverse-phase (250 x 4 mm, C18) column and UV, diode-array or MS detector. A linear gradient of acetic acid and acetonitrile provided excellent separation of glycoside and aglycone-phytoestrogens from kudzu root and soy preparations. The C18 cartridge extraction of serum yielded excellent recovery of both glycoside- and aglycone-phytoestrogens, while the trichloroacetic acid-methanol extraction yielded excellent recovery of glycoside but poor recovery of aglycone compounds. UV and MS detectors were suitable for phytoestrogen analysis in plant and serum samples, while the diode-array detector was suitable for generating the UV absorbance curve for phytoestrogens.
Cost-Effective Triple-Mode Reconfigurable Pipeline FFT/IFFT/2-D DCT Processor (2008)

This investigation proposes a novel radix-4 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> algorithm with the low computational complexity of a radix-16 algorithm but the lower hardware requirement of a radix-4 algorithm. The proposed pipeline radix-4 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> single delay feedback path (R4 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> SDF) architecture adopts a multiplierless radix-4 butterfly structure, based on the specific linear mapping of common factor algorithm (CFA), to support both 256-point fast Fourier transform/inverse fast Fourier transform (FFT/IFFT) and 8times8 2D discrete cosine transform (DCT) modes following with the high efficient feedback shift registers architecture. The segment shift register (SSR) and overturn shift register (OSR) structure are adopted to minimize the register cost for the input re-ordering and post computation operations in the 8times8 2D DCT mode, respectively. Moreover, the retrenched constant multiplier and eight-folded complex multiplier structures are adopted to decrease the multiplier cost and the coefficient ROM size with the complex conjugate symmetry rule and subexpression elimination technology. To further decrease the chip cost, a finite wordlength analysis is provided to indicate that the proposed architecture only requires a 13-bit internal wordlength to achieve 40-dB signal-to-noise ratio (SNR) performance in 256-point FFT/IFFT modes and high digital video (DV) compression quality in 8 times 8 2D DCT mode. The comprehensive comparison results indicate that the proposed cost effective reconfigurable design has the smallest hardware requirement and largest hardware utilization among the tested architectures for the FFT/IFFT computation, and thus has the highest cost efficiency. The derivation and chip implementation results show that the proposed pipeline 256-point FFT/IFFT/2D DCT triple-mode chip consumes 22.37 mW at 100 MHz at 1.2-V supply voltage in TSMC 0.13-mum CMOS process, which is very appropriate for the RSoCs IP of next-generation handheld devices.
AR/ER Ratio Correlates with Expression of Proliferation Markers and with Distinct Subset of Breast Tumors (2020)

The co-expression of androgen (AR) and estrogen (ER) receptors, in terms of higher AR/ER ratio, has been recently associated with poor outcome in ER-positive (ER+) breast cancer (BC) patients. The aim of this study was to analyze if the biological aggressiveness, underlined in ER+ BC tumors with higher AR/ER ratio, could be due to higher expression of genes related to cell proliferation. On a cohort of 47 ER+ BC patients, the AR/ER ratio was assessed by immunohistochemistry and by mRNA analysis. The expression level of five gene proliferation markers was defined through TaqMan<sup>®</sup>-qPCR assays. Results were validated using 979 BC cases obtained from gene expression public databases. ER+ BC tumors with ratios of AR/ER ≥ 2 have higher expression levels of cellular proliferation genes than tumors with ratios of AR/ER < 2, in both the 47 ER+ BC patients (<i>P</i> < 0.001) and in the validation cohort (<i>P</i> = 0.005). Moreover, BC cases with ratios of AR/ER ≥ 2 of the validation cohort were mainly assigned to luminal B and HER2-enriched molecular subtypes, typically characterized by higher proliferation and poorer prognosis. These data suggest that joint routine evaluation of AR and ER expression may identify a unique subset of tumors, which show higher levels of cellular proliferation and therefore a more aggressive behavior.
Effect of mast cell chymase inhibitor on the development of scleroderma in tight‐skin mice (2005)

1 Although the pathogenesis of scleroderma is not fully understood, activation of connective-tissue-type mast cells (CTMCs) has been implicated in various fibrotic diseases. 2 Our previous study showed that the number of CTMCs was markedly increased during fibrous proliferation in the skin of a scleroderma model, namely tight-skin (Tsk) mice. Because mast cells express numerous bioactive factors, such as cytokines, growth factors, proteases, and others, it is crucial to identify the primary factors that may be involved in the pathogenesis of scleroderma. Our previous study also showed that a CTMC-specific protease, chymase-4, was selectively upregulated in accordance with the development of skin fibrosis in Tsk mice. 3 To further elucidate the role of chymase secreted from CTMCs, we evaluated the therapeutic effects of a synthetic chymase-specific inhibitor, SUN-C8257, on the development of skin fibrosis in Tsk mice. SUN-C8257 (50 mg kg-1 day-1) was administered via intraperitoneal injection in 13-week-old Tsk mice for a period of 2 weeks. 4 Treatment with SUN-C8257 significantly reduced chymase activity by 43% and the chymase-4 mRNA level by 47%, and also decreased the thickness of the subcutaneous fibrous layer of Tsk mice by 42% compared with that of Tsk mice injected with vehicle. 5 Furthermore, immunohistochemical analysis revealed that transforming growth factor (TGF)-beta1 staining in the fibrous layer of Tsk skin was markedly reduced by the treatment with SUN-C8257. This chymase inhibitor may prevent the chymase-dependent pathway that activates the latent TGF-beta1 in fibrous tissue, and may exhibit beneficial effects that inhibit the development of fibrosis. 6 In conclusion, our results strongly support the assumption that CTMC-derived chymase may play a key role in the pathogenesis of scleroderma.
FrzA, a Secreted Frizzled Related Protein, Induced Angiogenic Response (2002)

These results showed that FrzA has proangiogenic effects and suggest that Wnt signaling may be involved in normal differentiation as well as in the pathological development of vasculature.
Competitive queueing policies for QoS switches (2003)

We consider packet scheduling in a network providing differentiated services, where each packet is assigned a value. We study various queueing models for supporting QoS (Quality of Service). In the nonpreemptive model, packets accepted to the queue will be transmitted eventually and cannot be dropped. The FIFO preemptive model allows packets accepted to the queue to be preempted (dropped) prior to their departure, while ensuring that transmitted packets are sent in the order of arrival. In the bounded delay model, packets must be transmitted before a certain deadline, otherwise it is lost (while transmission ordering is allowed to be arbitrary). In all models the goal of the buffer policy is to maximize the total value of the accepted packets.Let α be the ratio between the maximal and minimal value. For the non-preemptive model we derive a Θ(log &alpha) competitive ratio, both exhibiting a buffer policy and a general lower bound. For the interesting case of two distinct values, we give an 2α--1/α competitive buffer policy, which exactly matches the lower bound. We also analyze a RED-like policy and derive its competitive ratio, which is approximately 2α--0.5/α for two values and Θ(log α) for multiple values. In addition we improve the previous known lower and upper bounds of the Fixed Partition and Flexible Partition policies.For the FIFO preemptive model, we improve the general lower bound and show a tight bound for the special case of queue size 2. We prove that the bounded delay model with uniform delay 2 is equivalent to a modified FIFO preemptive model with queue size 2. We then give improved upper and lower bounds on the 2-uniform bounded delay model. We also give lower bound for the 2-variable bounded delay model, which matches the previously known upper bound.
Global governance through transnational network organizations - the scope and limitations of civil society self-organization (2004)

When the topic of global governance or post-national governance arises, it generally\ndoes so in the context of the co-operation between nation states, international\nagreements and the role of international organizations. As opposed to this, global\ngovernance through the self-organization of transnational civil society is rarely\ndiscussed. Therefore, the aim of this paper is to demonstrate the scope and limitations\nof global governance through civil society self-organization. The case of the\nâForest Stewardship Councilâ (FSC), which is now deemed a success, has been\nselected to demonstrate this phenomenon at work. What is involved here is a\nglobally distributed environmental label for the certification of sustainably managed\nforests. The FSC shows how a private civil society regime can be implemented,\nhow its implementation can be controlled and how violations can be\nsanctioned. It may be stated that the case of the Forest Stewardship Council is a\nform of global governance without nation-state involvement that can be viewed as a\ncomplete alternative to global governance through nation states.\nThe rapid spread of the FSC system was enhanced by the dynamic combination\nof civil society self-organization with market mechanisms. Moreover, the FSC\nsystem fills a gap that arose from the political failure at the level of international\nregimes. However, it has become clear that national forest protection standards are\nneeded for the FSC system to function smoothly. The FSC system cannot replace\nnational legislation and its implementation by an effective administration. The fact\nthat the FSC can rely not only on its own internal means of sanction (i.e. withdrawal\nof certification), but can also resort to boycotts as a potential external\ninstrument of sanction is undoubtedly a key factor behind the success of the FSC.\nHowever, the analysis also shows the limits of global governance through selforganization:\nAs no nation state has the norm-setting monopoly, the FSC system\ncompetes with other certification systems in many countries throughout the world.\nOverall, the FSC system can be deemed a success. Private standards appear to\nwork best if a specific combination of self-organization and market mechanisms\ncomes to fruition, if the non-state systems are embedded in nation-state systems, if\nresources are available outside the system that can, if necessary, be used to mobilize\nconsumers and if the problems that necessarily arise from the competition of\ncertification systems can be overcome.
Carnitine Deficiency of Human Skeletal Muscle with Associated Lipid Storage Myopathy: A New Syndrome (1973)

In a rare myopathy muscle fibers contained myriad lipid-filled vacuoles. Homogenates of the patient's muscle oxidized fatty acids more slowly than normal (11 controls). Addition of carnitine increased the oxidation rate with the patient's muscle to the level attained by the controls with carnitine. In five separate muscle samples from the patient the mean carnitine level was less than 20 percent of that observed in 42 controls. Carnitine palmityl transferase and palmityl thiokinase levels in the patient's muscles were not depressed. The present case represents the first recognized instance of carnitine deficiency in human skeletal muscle.
Experimental Observation of the Total Reflection by a Monodomain Cholesteric Liquid Crystal (1982)

The reflection spectra from a monodomain cholesteric liquid crystal are measured for obliquely incident light. The first order reflection region is found to be divided into three regions at a large angle of incidence. The central region shows high reflectivity irrespective of incident polarization and is attributed to the total reflection. The total reflection peak is also observed between the second order reflection peaks even at a small angle of incidence. The reflection spectra are numerically computed by the 4×4 matrix method and are in good agreement with the experiments.
A pulsed decimal technique for single-channel, dynamic signaling for IoT applications (2017)

Pulsed-Index Communication (PIC) is a recent technique for single-channel communication which is based on the principle of transferring the indices of only the ON bits in the form of a series of pulse streams. In this paper, we present a modified version of PIC which is based on the same underlying idea but with key improvements in data rate and reliability. The proposed technique is called Pulsed Decimal Communication (PDC). Like PIC, PDC is a protocol for single-channel, high-data rate, low-power dynamic signaling that does not require any clock and data recovery. It however achieves higher data rates by introducing a three-step algorithm, comprising a segmentation, an encoding, and a sub-segmentation step. The segmentation step is used to split the data word into smaller segments and therefore smaller decimal numbers to represent them. The encoding step reduces the number of ON bits in the data and relocates them to lower indices. The sub-segmentation step is used to split further the segments into smaller sub-segments. The complete process reduces the number of pulses required to transmit binary data, thus improving the data rate. Compared with PIC, PDC achieves a 78% improvement in data rate and is more reliable as it eliminates the variations in the number of symbols to be transmitted. An FPGA and an ASIC (65nm technology) implementation of the protocol show that the low-power operation and small footprint of PIC are maintained in PDC, which consumes around 25of power at a clock frequency of 25MHz with a gate count of approximately 2150.
Synthesis and Evaluation of Cu-SAPO-34 Catalysts for Ammonia Selective Catalytic Reduction. 1. Aqueous Solution Ion Exchange (2013)

SAPO-34 molecular sieves are synthesized using various structure directing agents (SDAs). Cu-SAPO-34 catalysts are prepared via aqueous solution ion exchange (IE). Catalysts are characterized with surface area/pore volume measurements, temperature programmed reduction (TPR), electron paramagnetic resonance (EPR), and nuclear magnetic resonance (NMR) spectroscopies. Catalytic properties are examined using standard ammonia selective catalytic reduction (NH3–SCR) and ammonia oxidation reactions. During solution IE, different SAPO-34 samples undergo different extent of structural damage via irreversible hydrolysis. Si content within the samples (i.e., Al–O–Si bond density) and framework stress are key factors that affect irreversible hydrolysis. Even using very dilute Cu acetate solutions, it is not possible to generate Cu-SAPO-34 samples with only isolated Cu2+ ions. Small amounts of CuOx species always coexist with isolated Cu2+ ions. Highly active and selective Cu-SAPO-34 catalysts for NH3-SCR are readily generated using this synthesis protocol, even for SAPO-34 samples that degrade substantially during solution IE. High-temperature aging is found to improve the catalytic performance. This is likely due to reduction of intracrystalline mass-transfer limitations via formation of additional porosity in the highly defective SAPO-34 particles formed after IE.
Naturalness and the Weak Gravity Conjecture (2014)

The weak gravity conjecture (WGC) is an ultraviolet consistency condition asserting that an Abelian force requires a state of charge q and mass m with q>m/m_{Pl}. We generalize the WGC to product gauge groups and study its tension with the naturalness principle for a charged scalar coupled to gravity. Reconciling naturalness with the WGC either requires a Higgs phase or a low cutoff at Λ∼qm_{Pl}. If neither applies, one can construct simple models that forbid a natural electroweak scale and whose observation would rule out the naturalness principle.
DS code acquisition in slowly fading multi-path channel (2002)

This paper presents analytical results of a direct sequence (DS) spread spectrum code acquisition, which is performed using a matched filter in a multipath channel. The performance measure is mean acquisition time, T/sub MA/. Mean acquisition times in a slowly, Rayleigh fading channel are presented. Constant false alarm rate criteria (CFAR) as a threshold setting rule is used. In a slowly fading channel, the mean acquisition time in a multipath channel is shorter than in a one-path channel. The case of equal average power of the path leads to the best result as opposed to a static channel. The advantage of selection diversity is therefore obtained in a frequency-selective fading channel.
Extracorporeal treatment for carbamazepine poisoning: Systematic review and recommendations from the EXTRIP workgroup (2014)

Despite the low quality of the available clinical evidence and the high protein binding capacity of carbamazepine, the workgroup suggested extracorporeal removal in cases of severe carbamazepine poisoning.
Abstract 2332: Oncogenic <i>MYD88</i> mutants require Toll-like receptors. (2013)

Abstract Oncogenic mutations affecting the signaling adapter MyD88 are present in 39% of activated B-cell-like (ABC) diffuse large B cell lymphomas (DLBCLs), with the most recurrent MyD88 mutant, L265P, present in 29% of cases. MYD88 mutations constitutively activate multiple signaling cascades that promote the survival and proliferation of ABC DLBCLs, including the NF-B, type-1 interferon, p38 and JAK/STAT pathways. It is unknown whether MyD88 mutants act autonomously or require a receptor to engage these downstream pathways. Here we show that the MyD88 L265P oncoprotein binds constitutively to two members of the Toll-like receptor family, TLR7 and TLR9, thereby amplifying signals that emanate from these receptors. Knockdown of TLR7 or TLR9 potently suppressed NF-B activity in ABC DLBCL cell lines and promoted apoptosis. Depletion of known proteins essential for TLR7 and TLR9 trafficking and signaling, including UNC93B1, PRAT4A or CD14, was lethal for ABC DLBCL lines. Similarly, pharmacologic inhibition of TLR7 and TLR9 function in lysosomal compartments using the cathepsin inhibitor zFA-fmk or hydroxychloroquine diminished MyD88 signaling and reduced survival of ABC DLBCL lines. TLR7 or TLR9 mutants that are defective in ligand binding failed to promote the survival of ABC DLBCL lines following knockdown of endogenous TLR7 or TLR9 expression in ABC DLBCL lines. Moreover, an inhibitory oligonucleotide capable of suppressing TLR9 responses in normal B cells blocked NF-B signaling and survival of ABC DLBCL lines. These new insights into the oncogenic mechanisms of MyD88 mutants provide a rationale for targeting of TLR7 and TLR9 signaling for the therapy of ABC DLBCL. Citation Format: Kian-Huat Lim, Gregory M. Barton, Louis M. Staudt. Oncogenic MYD88 mutants require Toll-like receptors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2332. doi:10.1158/1538-7445.AM2013-2332