gebhart/patrepeval huggingface dataset:
Sub-Graph Based Joint Sparse Graph for Sparse Code Multiple Access Systems (2018)

Sparse code multiple access (SCMA) is a promising air interface candidate technique for next-generation mobile networks, especially for massive machine-type communications. In this paper, we design a low-density parity-check (LDPC) coded SCMA detector by combining the sparse graphs of LDPC and SCMA into one joint sparse graph (JSG). In our proposed scheme, the SCMA sparse graph defined by small size indicator matrix is utilized to construct the JSG, which is termed as sub-graph-based JSG of SCMA (SG-JSG-SCMA). In this paper, we first study the binary-LDPC coded SG-JSG-SCMA system. To combine the SCMA variable node and LDPC variable node into one joint variable node, a nonbinary LDPC (NB-LDPC) coded SG-JSG-SCMA is also proposed. Furthermore, to reduce the complexity of NB-LDPC coded SG-JSG-SCMA, a joint trellis representation (JTR) is introduced to represent the search space of NB-LDPC coded SG-JSG-SCMA. Based on JTR, a low complexity joint trellis-based detection and decoding algorithm is proposed to reduce the computational complexity of the NB-LDPC coded SG-JSG-SCMA system. According to the simulation results, SG-JSG-SCMA brings significant performance improvement compare with the conventional receiver using the disjoint approach, and it can also outperform a turbo-structured receiver with comparable complexity. Moreover, the joint approach also has advantages in terms of processing latency compare with the turbo approaches.
Improving the Diagnosis of SIBO Using an At-Home Handheld App Connected Breath Analysis Device (AIRE) (2022)

INTRODUCTION Small Intestinal Bacterial Overgrowth (SIBO) is a common yet underdiagnosed condition. Lactulose hydrogen breath tests (LHBT) are typically used to detect SIBO; however, current breath testing methods require specialised, expensive equipment and technical support and are either done at a point-of-care facility and/or have to be mailed to a central laboratory. To address these issues a novel hand-held breath analyzer (AIRE ® , FoodMarble) was tested. The aims of this study were first, to perform a technical assessment of the AIRE device, second to compare the performance of the AIRE device against a commercially available mail-in LHBT kit using a zero-inflated negative binomial mixed effect model. METHODS Three AIRE devices were tested with certified test gases covering a diagnostically meaningful range (hydrogen mixed with air at 3 ppm, 10 ppm and 50 ppm). For the clinical study, 36 patients suspected to have SIBO presenting to a tertiary level clinic were provided with an AIRE device and performed concurrent LHBTs at home with a mail-in LHBT kit. RESULTS The overall average readings (mean ± SD) for the AIRE devices tested at 3 ppm, 10 ppm and 50 ppm H 2 were: 3.5 ± 0.7 ppm; 10.7 ± 1.1 ppm and 49.5 ± 2.6 ppm respectively. The overall mean absolute error across the tested devices was 1.2 ppm. A significant positive correlation (r = 0.78, p &lt; 0.001) was demonstrated between AIRE and mail-in kit H 2 values. DISCUSSION The AIRE device is a compelling alternative to mail-in LHBT kits for the diagnosis of SIBO. The AIRE device may also offer advantages over other traditional breath testing methods.
Methanol to Olefins Reaction over Cavity-type Zeolite: Cavity Controls the Critical Intermediates and Product Selectivity (2018)

Methanol to olefins (MTO) reaction over H-RUB-50 zeolite, an eight-membered ring (8-MR) and cavity-type zeolite, presents higher selectivity for ethene. The host–guest interaction was dissected and used to explain the cavity-controlled reaction route and product selectivity. By the aid of the in situ 13C MAS NMR spectroscopy, GC-MS, 12C/13C-methanol switch experiments, and theoretical calculations, the methylbenzenium cations, methylcyclopentenyl cations (triMB+, tetraMB+, and triMCP+), and their deprotonated forms with less methyl groups substitution were captured over LEV zeolite and confirmed as the critical reaction intermediates. The energetic span model was employed to identify the preferred reaction mechanism and provide the theoretical evidence to understand product selectivity. The side-chain methylation mechanism was theoretically predicated to be the energetically favorable route for olefins generation with the participation of these active intermediates. Paring cycle with trimethlycyclopentadienyl cation as the intermediate makes less contribution to ethene formation due to the relatively large energy span. Based on the overall evaluation of the catalytic cycle, the difference of energy span of the whole reaction pathway for ethene and propene formation can give direct theoretical evidence for product selectivity. Additional study to the steps for generating precursors of ethene and propene offers extra support on the understanding of product selectivity and the dominant generation of ethene. This study captured the critical intermediates and established a rational and energetically feasible route of light olefins generation from MTO reaction over H-RUB-50. More importantly, it is exhibited that cavity controls the product selectivity via the important steric constraint for the formation of critical intermediates and the proceeding of critical reaction steps, based on the understanding of the host–guest interaction of the cavity-type zeolite catalyzed MTO reaction.
Development of BLX-3030, a potent and selective inhibitor of CDK9 for the treatment of NMYC-driven NEPCS. (2023)

e17067 Background: Cell lineage reprogramming in cancer cells is a major mechanism for cancers to develop drug resistance and escape targeted therapy. The use of new potent targeted therapies in prostate cancers has led to the development of highly aggressive cancers, including neuroendocrine prostate cancer (NEPC).Gene amplification of N-MYC and C-MYC oncogenes leads to its overexpression in NEPC and mCRPC patients. This overexpression is highly prevalent in these lethal subtypes of cancers, detected in 2% of all Prostate Cancers (PCa) and over 10-17% of mCRPC patients. N-MYC is a transcriptional target of CDK9, which acts as an oncogenic driver, sufficient to transform human-derived prostate cancer cells to take on NEPC phenotypic changes. This results in a more aggressive disease identified in late-stage human PCa patients. Additionally, N-MYC and C-MYC are required for tumor drug resistance and its downregulation, through CDK9 inhibition, lowers tumor growth. Our efforts have demonstrated that targeting both N-MYC and C-MYC as a driver of NEPC and mCRPC with a highly selective CDK9 inhibitor (BLX-3030) is a viable approach for therapeutic intervention of mCRPC and NEPC. Methods: We employed our AI/ML driven FIELDS fragment-based design strategies, in vitro including FACS/apoptosis, cell migration, live cell imaging, immunofluorescent and in vivo tumor models, 7-day tox, PK, selectivity, and ADME-Tox and in vitro safety and secondary pharmacological assays. Results: We discovered and synthesized a series of novel small molecule CDK9 agents that reversibly bind to CDK9, competitively block the ATP site with an IC 50 of &lt; 5 nM, and elicit pharmacological responses in N-MYC, C-MYC, and other prostate cancer cells in vitro and in vivo. We detected the expression of CDK9 and N-MYC in PC-3, DU-145, LNCaP, LASCPC-01, NCI-H660, and 22RV1 cell lines. BLX-3030 exhibited potent cellular efficacy in PC cells (IC 50 of 22 to 590 nM) and in N-MYC expressed cells (IC 50 of 76, 470, and 132 nM), respectively. BLX-3030 reduced pCDK9, C-MYC, Mcl-1, N-MYC and its downstream RNA Pol II (Ser-2) and pAR (Ser-81) in a dose dependent manner. Additionally, we performed FACS/apoptosis, cell migration, and live cell imaging, including immunofluorescence. We also conducted three separate in vivo efficacy mouse models (LASCPC-01, 22RV1, and C4-2) which demonstrated &gt; 70% TGI. Several in vitro ADME-Tox, hERG, P450, safety panel screen, in vivo MTD and dose range finding experiments in SD rats and beagle dogs will also be presented. Conclusions: In summary, a series of BLX-3030 and its analogs display a potency in MYC-driven PCa, with ideal PK properties in rodent, canine species ranging 28-82 % F, with low clearance, and &gt; 3.0 hr half-life. Within this profile, BLX-3030 was selected as a candidate that had the appropriate developable properties. Our plans for IND enabling studies and future clinical trials will also be discussed.
The functional MDM2 SNP309 polymorphism is associated with an earlier age of diagnosis in women with lung cancer (2007)

10550 Background: MDM2 protein is a key negative regulator of p53 protein by targeting its destruction through the ubiquitin pathway. A single nucleotide polymorphism (SNP309 T→G) has been identified in the promoter of the MDM2 gene which results in higher levels of MDM2 protein, attenuation of the p53 pathway, and enhanced tumorigenesis. Estrogen signaling has also been shown to upregulate MDM2 expression. Recent studies have suggested that the MDM2 SNP309 polymorphism is associated with earlier age of onset of certain cancers, particularly in women. The purpose of this study was to determine whether the MDM2 SNP309 polymorphism is associated with lung cancer risk in a gender specific manner. Methods: MDM2 genotype analysis was performed on a cohort of 115 consecutive Caucasian patients with histologically confirmed lung cancer using a PCR-based nucleotide polymorphism discrimination test. Allele status was described as homozygous wild-type (TT), homozygous variant (GG) and heterozygous variant/wild-type (TG). Results: In total, 46 female and 69 male lung cancer patients were screened for the MDM2 SNP309 polymorphism ( Table 1 ). Females with the GG genotype were diagnosed at a significantly earlier age as compared to females with the TT genotype (p=0.038), while a similar comparison for males showed no significant difference. A trend towards an earlier age of onset in females as compared to males with the GG genotype was observed, although the sample size was small and this was not significant (p=0.47). Conclusions: In this study, we found that women, but not men, with the MDM2 SNP309 GG genotype were particularly susceptible to the development of lung cancer at an earlier age, supporting the hypothesis that the expression of this polymorphism is gender-specific and possibly regulated by estrogen. Women with the MDM2 polymorphism represent a potential high-risk group for the focus of lung cancer screening and chemoprevention efforts with anti-estrogen therapy. [Table: see text] No significant financial relationships to disclose.
Hybrid Quantum Circuit with a Superconducting Qubit Coupled to a Spin Ensemble (2011)

We report the experimental realization of a hybrid quantum circuit combining a superconducting qubit and an ensemble of electronic spins. The qubit, of the transmon type, is coherently coupled to the spin ensemble consisting of nitrogen-vacancy centers in a diamond crystal via a frequency-tunable superconducting resonator acting as a quantum bus. Using this circuit, we prepare a superposition of the qubit states that we store into collective excitations of the spin ensemble and retrieve back into the qubit later on. These results constitute a proof of concept of spin-ensemble based quantum memory for superconducting qubits.
Impact of sleeve gastrectomy and dietary change on metabolic and hepatic function in an obesity rat model - Experimental research (2020)

HF for 15 weeks induced obesity with metabolic syndrome and NAFLD in rats. SG and dietary intervention improved metabolic state and NAFLD; however, their combination was significantly more effective.
Should the Charter Apply to Universities (2015)

This article explores the unresolved issue of whether the Charter of Rights and Freedoms applies to public universities in Canada. The author considers the Supreme Court’s judgment in McKinney v. University of Guelph in the context of more recent jurisprudence on the application of the Charter, as well as divergent lower court judgments concerning restrictions on student expression. He argues that public universities in Alberta, British Columbia, and Ontario implement specific government policies and exercise statutory powers of a public nature, which should subject them constitutional scrutiny. He further demonstrates that the Charter’s application is reconcilable with institutional autonomy. By limiting constitutional review to the public decisions of universities and imposing the reasonableness standard, courts can protect Charter values without unduly intruding into operational activities. More fundamentally, the author argues that the continued treatment of universities as Charter-free zones is both indefensible as a matter of legal principle, and inconsistent with the preservation of academic freedom.
Interleukine-2 Therapy Does Not Increase the Risk of Hodgkin or Non-Hodgkin Lymphoma in HIV-Infected Patients: Results From FHDH ANRS CO4 (2009)

In this large observational study, IL-2 therapy did not increase the risk of lymphoma, either NHL or HL, in HIV-infected patients.
An Automatic Molecular Diagnosis Approach Based on Boosting Classification for ALS disease. (2005)

It has always been accepted dogma that the deleterious effects of ionising radiation such as mutagenesis and carcinogenesis are due mainly to direct damage to DNA. Using the Columbia University charged-particle microbeam and the highly sensitive AL cell mutagenic assay, it is shown here that non-irradiated cells acquire the mutagenic phenotype through direct contact with cells whose nuclei are traversed with 2 alpha particles each. Pre-treatment of cells with lindane, a gap junction inhibitor, significantly decreased the mutant yield. Furthermore, when irradiated cells were mixed with control cells in a similar ratio as the in situ studies, no enhancement in bystander mutagenesis was detected. Our studies provide clear evidence that genotoxic damage can be induced in non-irradiated cells, and that gap junction mediated cell-cell communication plays a critical role in the bystander phenomenon.
E-002 Safety of Retained Microcatheters: An Evaluation of RF Heating in a Nitinol Braided Endovascular Catheter at 1.5T and 3T (2013)

<h3>Purpose</h3> The use of ethylene-vinyl alcohol copolymer (EVOH, Onyx) for liquid embolisation of cranial vascular lesions has occasionally resulted in microcatheter fragments unintentionally remaining <i>in situ</i> in patients following endovascular procedures. Undergoing subsequent diagnostic MRI examinations poses a safety concern due to potential radiofrequency (RF) heating mediated by the metallic braid incorporated into the microcatheter. We sought to assess heating of a microcatheter commonly used to deliver Onyx in a phantom. <h3>Methods</h3> A 1.9F nitinol braided microcatheter (eV3 Echelon™-14, Irvine, CA) was embedded in a polyacrylamide phantom with five fluoroptic temperature probes placed along the length of the microcatheter and an additional background sensor. The phantom was scanned using a fast spin echo (FSE) sequence at average specific absorption rate (SAR) levels from 0.25 to 4.0 W/kg. Further scanning was performed using 2-minute clinical scans: T1 FSE, T2 FSE, DWI, T2 FLAIR, 3D-SPGR and b-SSFP. The scan that produced the most heating was repeated over a 15-minute acquisition. The experiments were then repeated with catheter fragment lengths of 9cm, 18cm, 36cm and 72cm. Experiments were performed on both 1.5T (Philips Achieva, Cleveland, OH) and 3T (GE Discovery 750w, Milwaukee, WI) clinical scanners. <h3>Results</h3> The maximal heating for the nitinol braided catheter immersed 93cm occurred at 20cm proximal to the tip using the T1 FSE sequence at 1.5 T. Maximal heating at 3T occurred using the b-SSFP sequence at the same position. The maximal temperature rise during a 2-minute scan was 0.84C at 1.5T and 0.45C at 3T. Figure 1 shows the temperature changes along different points on the catheter during a 15-minute T1 FSE sequence at 1.5T. The same scans for fragment lengths of 9cm, 18cm, 36cm and 72cm produced maximal temperature (C) rises of 0.68, 0.80, 1.70 and 1.07 at 1.5T, respectively. The temperature changes during a 15-min b-SSFP sequence at 3T for these fragment lengths were 0.66, 0.83, 1.07 and 0.72, respectively. <h3>Conclusions</h3> Heating of nitinol braided microcatheters occurred during diagnostic MR scanning and was a function of SAR level and geometric considerations. SAR and time limitations are proposed for patients with this microcatheter entrapped in their vasculature. Although the catheter displayed higher heating levels at 1.5T relative to 3T at a given SAR, it should be noted that there are most likely differences between the SAR models on the two scanner interfaces. Furthermore, the 3T scanner used for this study had a wider diameter bore. <h3>Disclosures</h3> A. Losey: None. P. Lillaney: None. A. Martin: None. V. Halbach: None. D. Cooke: None. C. Dowd: None. R. Higashida: None. D. Saloner: None. M. Wilson: None. M. Saeed: None. S. Hetts: None.
ChemInform Abstract: Total Synthesis of Clavosolide A. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Recovery of 3-D Motion from Time-Varying Image Flows (1996)

In this paper we deal with the problem of recovering 3-D motion and structure from a time-varying 2-D velocity vector field. A great deal has been done on this topic, most of which has concentrated on finding necessary and sufficient conditions for there to be a unique 3-D solution corresponding to a given 2-D motion. While previous work provides useful theoretical insight, in most situations the known algorithms have turned out to be too sensitive to be of much practical use. It appears that any robust algorithm must improve the 3-D solution over time. As a step toward such algorithm, we present a method for recovering 3-D motion and structure from a given time-varying 2-D velocity vector field. The surface of the object in the scene is assumed to be locally planar. It is also assumed that 3-D velocity vectors are piecewise constant over three consecutive frames (or two snapshots of flow field). Our farmulation relates 3-D motion and object geometry with the optical flow vector as well as its spatial and temporal derivatives. The linearization parameters, or equivalently. the first-order flow approximation (in space and time) is sufficient to recover rigid body motion and local surface structure from the local instantaneous flow field. We also demonstrate. through a sensitivity analysis carried out for synthetic and natural motions in space. that 3-D motion can be recovered reliably.
TheC. elegansT-type calcium channel CCA-1 boosts neuromuscular transmission (2005)

Low threshold-activated or T-type calcium channels are postulated to mediate a variety of bursting and rhythmic electrical firing events. However, T-type channels' exact physiological contributions have been difficult to assess because of their incompletely defined pharmacology and the difficulty in isolating T-type currents from more robust high threshold calcium currents. A current in C. elegans pharyngeal muscle displays the kinetic features of a T-type calcium channel and is absent in animals homozygous for mutations at the cca-1 locus (see accompanying paper). cca-1 is expressed in pharyngeal muscle and encodes a protein (CCA-1) with strong homology to the alpha1 subunits of vertebrate T-type channels. We show that CCA-1 plays a critical role at the pharyngeal neuromuscular junction, permitting the efficient initiation of action potentials in response to stimulation by the MC motor neuron. Loss of cca-1 function decreases the chance that excitatory input from MC will successfully trigger an action potential, and reduces the ability of an animal to take in food. Intracellular voltage recordings demonstrate that when wild-type cca-1 is absent, the depolarizing phase of the pharyngeal action potential tends to plateau or stall near -30 mV, the voltage at which the CCA-1 channel is likely to be activated. We conclude that the CCA-1 T-type calcium channel boosts the excitatory effect of synaptic input, allowing for reliable and rapid depolarization and contraction of the pharyngeal muscle. We also show that the pharyngeal muscle employs alternative strategies for initiating action potentials in certain cases of compromised MC motor neuron function.
Neutralization of granulocyte macrophage colony-stimulating factor decreases amyloid beta 1-42 and suppresses microglial activity in a transgenic mouse model of Alzheimer's disease (2009)

The purpose of our study was to investigate microglia and astrocytes that are associated with human mutant amyloid precursor protein and amyloid beta (Abeta). We investigated whether the anti-granulocyte-macrophage-colony stimulating factor (GM-CSF) antibody can suppress microglial activity and decrease Abeta production in Alzheimer's disease transgenic mice (Tg2576 line). An antibody to mouse GM-CSF was introduced by intracerebroventricular (ICV) injections into the brains of 10-month-old Tg2576 male mice. We assessed the effect of several GM-CSF-associated cytokines on microglial activities and their association with Abeta using quantitative real-time RT-PCR, immunoblotting, immunohistochemistry analyses in anti-GM-CSF antibody-injected Tg2576 mice. Using sandwich ELISA technique, we measured intraneuronal Abeta in Tg2576 mice injected with GM-CSF antibody and PBS vehicle-injected control Tg2576 mice. Using double-labeling immunofluorescence analysis of intraneuronal Abeta, Abeta deposits and pro-inflammatory cytokines, we assessed the relationship between Abeta deposits and microglial markers in the Tg2576 mice, and also in the anti-GM-CSF antibody-injected Tg2576 mice. Our real-time RT-PCR analysis showed an increase in the mRNA expression of IL6, CD11c, IL1beta, CD40 and CD11b in the cerebral cortices of the Tg2576 mice compared with their littermate non-transgenic controls. Immunohistochemistry findings of microglial markers agreed with our real-time RT-PCR results. Interestingly, we found significantly decreased levels of activated microglia and Abeta deposits in anti-GM-CSF antibody-injected Tg2576 mice compared with PBS vehicle-injected Tg2576 mice. Findings from our real-time RT-PCR and immunoblotting analysis agreed with immunohistochemistry results. Our double-labeling analyses of intraneuronal Abeta and CD40 revealed that intraneuronal Abeta is associated with neuronal expression of CD40 in Tg2576 mice. Our quantitative sandwich ELISA analysis revealed decreased levels of soluble Abeta1-42 and increased levels of Abeta1-40 in Tg2576 mice injected with the anti-GM-CSF antibody, suggesting that anti-GM-CSF antibody alone decreases soluble Abeta1-42 production and suppresses microglial activity in Tg2576 mice. These findings indicating the ability of the anti-GM-CSF antibody to reduce Abeta1-42 and microglial activity in Tg2576 mice may have therapeutic implications for Alzheimer's disease.