gebhart/patrepeval huggingface dataset:
Temporal and Spatial Differences in Crop Yields of a Mature Silver Maple Alley Cropping System (2014)

Although alley cropping practices improve ecosystem services, they can reduce crop yields, especially at the tree‐crop interface and progressively at increasing distances from that interface with time. The objective of this study was to evaluate temporal and spatial yield differences in a no‐till corn ( Zea mays L.)–soybean [ Glycine max (L.) Merr.] rotation in a mature (11–19 yr) silver maple ( Acer saccharinum L.) alley cropping system in the claypan region of the temperate climatic zone. Silver maple saplings were planted in 20 m wide rows at 3.6 m spacing between trees in 1990. Crop yields were measured at 3.3, 6.7, and 10 m distances from the tree row from 2001 to 2008. Corn yields in 2002, 2004, 2006, and 2008 and soybean yields in 2001, 2003, 2005, and 2007 were determined using a small plot combine and analyzed in a split‐plot in space and time design. Corn yield was 86 and 24% lower at 3.3 and 6.7 m compared to 10 m. The greatest reductions were recorded in 2006 when the site recorded the greatest yields. Late planting may have affected the corn yield despite 156% of the normal rain in 2008. Soybean yield was 77 and 24% lower at 3.3 and 6.7 m, respectively, compared to yield at 10 m. Soybean yields declined over time at all three measured distances. A reduction of competition and selection of drought and shade tolerant crops may help increase productivity while providing ecosystem services of the perennial tree rows.
Molecular simulations reveal a mechanism for enhanced allosteric coupling between voltage-sensor and pore domains in KCNQ1 explaining its activation by ML277 (2022)

Abstract The voltage-gated potassium channel KCNQ1 (K V 7.1) is important for the repolarizing phase of the cardiac action potential. Activators of KCNQ1 may provide a strategy for the pharmacological treatment of congenital long QT syndrome, a genetic disorder caused by pathogenic variants in KCNQ1 that promote arrhythmia susceptibility and elevate risk for sudden cardiac death. The small-molecule agonist ML277 recovers function of mutant KCNQ1 channels in human induced pluripotent stem cell-derived cardiomyocytes and could represent a starting point for drug development. Here we investigated ML277 mode of action by developing a molecular model of the KCNQ1-ML277 interaction corroborated by experimental and computational analyses. Ligand docking and molecular dynamics simulation demonstrated that ML277 binds to the interface between the voltage sensor and pore domains in KCNQ1. Model predicted binding energies for ML277 and 62 chemical analogs of ML277 correlated with EC 50 data available for these compounds. We identified novel ML277-interacting residues on the S5 and S6 segments of KCNQ1 by performing MM/PBSA energy calculations and site-directed mutagenesis of KCNQ1 coupled to electrophysiological characterization of the generated channel mutants. Network analysis of the molecular dynamics simulations further showed that ML277 increases the allosteric coupling efficiency between residues in the voltage sensor domain and residues in the pore domain. Derivatives of ML277 that are not active on KCNQ1 fail to increase allosteric coupling efficiency in the computational simulations. Our results reveal atomic details of the ML277 modulation of KCNQ1 activation. These findings may be useful for the design of allosteric modulators of KCNQ1 and other KCNQ channels that bind at the membrane-accessible protein surface. Statement of Significance The potassium ion channel KCNQ1 contributes to the generation of electrical impulses in the heart. Heritable mutations in KCNQ1 can cause channel loss-of-function and predispose to a life-threatening cardiac arrhythmia. Small molecules that bind KCNQ1 and enhance channel function could establish a novel anti-arrhythmic drug paradigm. We used molecular simulations to investigate how a small agonist of KCNQ1 (ML277) binds to the KCNQ1 channel and increases its function. We identified amino acids that are responsible for ML277 binding and show how ML277 promotes signaling in KCNQ1 and channel opening. This work advances our understanding how KCNQ1 and possibly other potassium channels can be activated with small molecules. These data provide a framework for drug development studies.
The effect of electrode placement and pulsewidth on asystole and bradycardia during the electroconvulsive therapy stimulus (2010)

Electroconvulsive therapy (ECT) is the most effective treatment for severe depression, and different forms are increasingly used in clinical practice. This study investigated the acute cardiac effects of different forms of ECT: bitemporal and bifrontal (1.5 times seizure threshold), and right unilateral (RUL) (five times seizure threshold). For RUL ECT, the effect of stimulus pulsewidth (1.0 or 0.3 ms) was also examined. Electrocardiograms recorded just prior to and during the ECT stimulus in 476 ECT treatments in 114 patients were examined. The degree of bradycardia (any slowing of heart rate) and incidence of asystole (absence of heart beats for ≥5 s) during the ECT stimulus were measured from these traces. Regression analyses estimated the contribution of patient and ECT treatment factors to the risk of bradycardia and asystole. Bifrontal ECT was associated with less severe bradycardia than bitemporal or RUL ECT (p<0.001). Modelling showed, for a mean pre-ECT heart rate of 85 beats per minute (bpm), expected heart rates during the stimulus were 78 bpm (bifrontal), 46 bpm (bitemporal) and 35 bpm (RUL). Bifrontal ECT was also associated with a lower incidence of asystole than RUL ECT (corrected odds ratio 1:207) and bitemporal ECT (corrected odds ratio 1:24). Ultrabrief pulsewidth stimulation resulted in lesser bradycardia and asystole than standard pulsewidth stimulation for RUL ECT. Modelling showed, for a mean pre-ECT heart rate of 86 bpm, expected heart rates were 43 bpm (ultrabrief RUL) and 26 bpm (RUL). Bradycardia and asystole were relatively common side-effects during the ECT stimulus. Bifrontal ECT was associated with the lowest risk of bradycardia and asystole during ECT and should be considered for patients at risk of arrhythmias and prolonged asystole during ECT.
Distributed Detection And Estimation In Decentralized Sensor Networks: An Overview (2006)

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006
Compositional Features of HDL Particles Interact with Albuminuria to Modulate Cardiovascular Disease Risk (2019)

Lipoproteins containing apolipoprotein B modify associations of elevated urinary albumin excretion (UAE) with cardiovascular disease (CVD). Additionally, it is known that elevated UAE alters high-density lipoprotein functionality. Accordingly, we examined whether HDL features might also modify UAE-associated CVD. Multivariable Cox proportional-hazards modeling was performed on participants of the PREVEND (Prevention of Renal and Vascular Endstage Disease) study at the baseline screening with standard lipid/lipoprotein analyses and, three-to-four years later (second screen), with nuclear magnetic resonance lipoprotein analyses focusing on HDL parameters including HDL particle (HDL-P) and apolipoprotein A-I concentrations. These were used with UAE and derived measures of HDL apoA-I content (apoA-I/HDL-C and apoA-I/HDL-P) in risk models adjusted for gender, age, apoB, diabetes, past CVD history, CRP and GFR. Interaction analysis was also performed. Baseline screening revealed significant associations inverse for HDL-C and apoA-I and direct for apoA-I/HDL-C. The second screening demonstrated associations inverse for HDL-P, large HDL-P, medium HDL-P, HDL size, and apoA-I/HDL-P. Significant interactions with UAE included apoA-I/HDL-C at the baseline screening, and apoA-I/HDL-P and medium HDL-P but not apoA-I/HDL-C at the second screening. We conclude that features of HDL particles including apoA-I/HDL-P, indicative of HDL apoA-I content, and medium HDL-P modify associations of elevated UAE with CVD risk.
Nonlocal edge state transport in the quantum spin Hall state (2009)

We present direct experimental evidence for nonlocal transport in HgTe quantum wells in the quantum spin Hall regime, in the absence of any external magnetic field. The data conclusively show that the non-dissipative quantum transport occurs through edge channels, while the contacts lead to equilibration between the counter-propagating spin states at the edge. We show that the experimental data agree quantitatively with the theory of the quantum spin Hall effect.
Determining Whether Agonist Density or Agonist Number Is More Important for Immune Activation via Micoparticle Based Assay (2020)

It is unknown if surface bound toll-like-receptor (TLR) agonists activate cells via density or total molecular number. To answer this question, we developed a TLR agonist surface conjugated polystyrene microparticle (MP) system. Using a library of MPs with varying TLR agonist density and number, we simultaneously observed innate immune cell MP uptake and TNFα expression using ImageStream flow cytometry on a cell by cell basis. The data shows that total TLR number and not density drives cellular activation with a threshold of approximately 10<sup>5</sup>-10<sup>6</sup> TLR agonists. We believe that this information will be crucial for the design of particulate vaccine formulations.
Clinical safety and efficacy of enfuvirtide (T-20), a new fusion inhibitor. A review of the presentation at the satellite symposium "New hope: advancing care in HIV infection" at the 15th annual Association of Nurses in AIDS Care conference, November 2002. (2003)

Proof of the concept that a fusion inhibitor could mediate clinically significant antiviral responses came from the demonstration that patients receiving 100 mg of enfuvirtide daily as monotherapy for 14 days achieved a mean reduction in viral load of 1.5 log10 copies/mL. Phase 2 studies established subcutaneous injection of 100 mg of enfuvirtide twice daily as the dosage of choice. In pivotal phase 3 trials, enfuvirtide was added to an optimized background regimen in heavily treatment-experienced patients. Virologic and immunologic responses were significantly better in patients receiving enfuvirtide in addition to optimized background regimens than in those receiving optimized background alone, with the incremental reduction in viral load between arms being 0.934 log10 copies/mL after 24 weeks of therapy. Subgroup analyses demonstrated this benefit to be similar regardless of age, sex, race, and baseline viral load. Enfuvirtide was well tolerated, with injection site reactions being the most common adverse event, although they were rarely treatment-limiting.
Polyphenols with Antiulcerogenic Action from Aqueous Decoction of Mango Leaves (Mangifera indica L.) (2009)

This study was designed to determine the gastroprotective effect of a Mangifera indica leaf decoction (AD), on different experimental models in rodents. The administration of AD up to a dose of 5 g/kg (p.o.) did not produce any signs or symptoms of toxicity in the treated animals, while significantly decreasing the severity of gastric damage induced by several gastroprotective models. Oral pre-treatment with AD (250, 500 or 1000 mg/kg) in mice and rats with gastric lesions induced by HCl/ethanol, absolute ethanol, non-steroidal anti-inflammatory drug (NSAID) or stress-induced gastric lesions resulted in a significant decrease of said lesions. Phytochemical analyses of AD composition demonstrated the presence of bioactive phenolic compounds that represent 57.3% of total phenolic content in this extract. Two main phenolic compounds were isolated, specifically mangiferin (C-glucopyranoside of 1,3,6,7-tetrahydroxyxanthone) and C-glucosyl-benzophenone (3-C-β-D-glucopyranosyl-4’,2,4,6-tetrahydroxybenzophenone). These findings indicate the potential gastroprotective properties of aqueous decoction from M. indica leaves.
Supplementary Table S1 from Combination of Ribociclib with BET-Bromodomain and PI3K/mTOR Inhibitors for Medulloblastoma Treatment <i>In Vitro</i> and <i>In Vivo</i> (2023)

&lt;p&gt;Supplementary Table S1&lt;/p&gt;
Handbook of Pharmaceutical Natural Products. By Goutam Brahmachari. (2010)

Wiley-VCH, Weinheim 2010. XX+926 pp. (2 volumes), hardcover € 349.00.—ISBN 978-3-527-32148-3
Pretreatment lesional volume impacts clinical outcome and thrombectomy efficacy (2018)

Pretreatment lesional volume is an independent predictor for functional outcome in acute ischemic stroke with proximal intracranial occlusion. The clinical benefit of adding mechanical thrombectomy to thrombolysis decreased with the increase of lesional volume. Ann Neurol 2018;83:178-185.
Adaptive Power and Resource Allocation Strategies for Green Radio (2011)

This paper presents a number of key radio resource management strategies across physical (PHY) and medium access control (MAC) layers for reducing base station energy consumption including power efficient link adaptation (LA), exploitation of multi-user diversity and trading bandwidth for energy efficiency. By collectively taking advantage of these radio resource management strategies, a multi-user adaptive power and resource allocation algorithm is proposed to ease the power requirements of a base station, whilst maintaining the same levels of service. The scheduling algorithm is evaluated within a LTE downlink simulator for various traffic load conditions. The results show that the proposed algorithm achieves a significant energy saving over a conventional non-energy aware resource allocation scheme.
Striking the Right Balance: Recall Loss for Semantic Segmentation (2021)

Class imbalance is a fundamental problem in computer vision applications such as semantic segmentation. Specifically, uneven class distributions in a training dataset often result in unsatisfactory performance on under-represented classes. Many works have proposed to weight the standard cross entropy loss function with pre-computed weights based on class statistics, such as the number of samples and class margins. There are two major drawbacks to these methods: 1) constantly up-weighting minority classes can introduce excessive false positives in semantic segmentation; 2) a minority class is not necessarily a hard class. The consequence is low precision due to excessive false positives. In this regard, we propose a hard-class mining loss by reshaping the vanilla cross entropy loss such that it weights the loss for each class dynamically based on instantaneous recall performance. We show that the novel recall loss changes gradually between the standard cross entropy loss and the inverse frequency weighted loss. Recall loss also leads to improved mean accuracy while offering competitive mean Intersection over Union (IoU) performance. On Synthia dataset, recall loss achieves $9\%$ relative improvement on mean accuracy with competitive mean IoU using DeepLab-ResNet18 compared to the cross entropy loss. Code available at https://github.com/PotatoTian/recall-semseg.
Processor allocation algorithm based on Frame Combing with Memorization for 2D mesh CMPs (2012)

Processor Allocator (PA) is one of the main components to achieve high performance Chip Multiprocessors (CMPs). The task of the PA is to assign a set of processors to execute an incoming job scheduled by the Operating System (OS). An efficient PA is one that allocates an incoming job, if a suitable free submesh exists, with minimum overhead. In this paper, we propose a new contiguous processor allocation algorithm, Frame Combing with Memorization (FCM) for 2D mesh CMPs, which is fast, has complete submesh recognition, and assigns a set of processors without creating coverage areas for the incoming job. Our proposed algorithm outperforms other existing allocation strategies based on busy array approach such as Improved First Fit (IFF), and Better First Fit (BFF), or even Right of Busy Submeshes (RBS), a fast busy list based PA algorithm. Performance evaluation has been done with different job sets over different network sizes and at different network occupations. Our proposed PA is in average 3 up to 5 times faster than IFF, BFF and RBS for allocating small job (size 4×2) in a network size 10×10. For big network sizes (30×30), it is up to 60, 79, and 48 times faster than IFF, BFF, and RBS, respectively.
Low levels of neurocognitive impairment detected in screening HIV-infected men who have sex with men: The MSM Neurocog Study (2016)

This study aimed to determine the prevalence of HIV neurocognitive impairment in HIV-infected men who have sex with men aged 18-50 years, using a simple battery of screening tests in routine clinical appointments. Those with suspected abnormalities were referred on for further assessment. The cohort was also followed up over time to look at evolving changes. HIV-infected participants were recruited at three clinical sites in London during from routine clinical visits. They could be clinician or self-referred and did not need to be symptomatic. They completed questionnaires on anxiety, depression, and memory. They were then screened using the Brief Neurocognitive Screen (BNCS) and International HIV Dementia Scale (IHDS). Two hundred and five HIV-infected subjects were recruited. Of these, 59 patients were excluded as having a mood disorder and two patients were excluded due to insufficient data, leaving 144 patients for analysis. One hundred and twenty-four (86.1%) had a normal composite z score (within 1 SD of mean) calculated for their scores on the three component tests of the BNCS. Twenty (13.9%) had an abnormal z score, of which seven (35%) were symptomatic and 13 (65%) asymptomatic. Current employment and previous educational level were significantly associated with BNCS scores. Of those referred onwards for diagnostic testing, only one participant was found to have impairment likely related to HIV infection. We were able to easily screen for mood disorders and cognitive impairment in routine clinical practice. We identified a high level of depression and anxiety in our cohort. Using simple screening tests in clinic and an onward referral process for further testing, we were not able to identify neurocognitive impairment in this cohort at levels consistent with published data.
Proposal of data-driven processor architecture Qv-K1 (2003)

This paper presents an extended SIMD form data operation for multi-media signal processing and a performance evaluation of data-driven processor Qv-K1. By appending proposed data-parallel operation mechanism, the number of executed instructions is reduced compared to SIMD. The processing ability of this processor could be increased.
Synthesis of α,α-Disubstituted Benzocyclobutane Amino Acids through [2+2] Annulation of Benzyne with Dehydroalanine (2020)

A mild and general method for the synthesis of α,α-disubstituted benzocyclobutane amino acids through a [2+2] annulation of benzyne with dehydroalanine is described. Yields up to 88% of the constrained quaternary amino acids can be obtained and its application in peptidomimetic synthesis is demonstrated.
Modulation of expression of genes encoding nuclear proteins following exposure to JANUS neutrons or {gamma}-rays (1994)

revealed induction of transcripts for c-jun, H4-histone, and (to a lesser extent) Rb following {gamma}-ray but not following neutron exposure. Expression of p53 and c-myc genes was unaffected by radiation exposure. Radiations at different doses and dose rates were compared for each of the genes studied.
Optimum Grip of a Polygon (1989)

It has been shown by Baker, Fortune and Grosse that any two-dimensional polygonal object can be prehended stably with three fingers, so that its weight (along the third dimension) is balanced. Besides, in this paper we show that form closure of a polygon object can be achieved by four fingers (previous proofs were not complete). We formulate and solve the problem of finding the optimum stable grip or form closure of any given polygon. For stable grip it is most natural to minimize the forces needed to balance through friction the object''s weight along the third dimension. For form closure, we minimize the worst-case forces needed to balance any unit force acting on the center of gravity of the object. The mathematical techniques used in the two instances are an interesting mix of Optimization and Euclidean geometry. Our results lead to algorithms for the efficient computation of the optimum grip in each case.
Randomised double blind controlled trial of cyclosporin in multiple sclerosis. (1989)

In a 2 year double blind controlled trial of cyclosporin against placebo in multiple sclerosis conducted at two centres there was a beneficial effect of the therapy upon the progression of the disease, relapse rate and relapse severity at one of the centres where the patients received a mean dose of 7.2 mg/kg/day. This beneficial effect was not seen in the other centre where a lower dose (mean 5 mg/kg/day) was given. Reduction in clinical progression was accompanied by decreased IgG synthesis in the central nervous system. Side effects included hypertension, renal insufficiency and anaemia and were of such severity to preclude the use of cyclosporin in a high enough dose to alter the course of the disease.
Development of an improved microneutralization assay for respiratory syncytial virus by automated plaque counting using imaging analysis (2005)

Our results demonstrate that the semi-automated assay is rapid and reliable. It provides results within two fold to the classical plaque microneutralization assay and is readily applied to the evaluation of neutralizing antibody titers in sera obtained from epidemiology or vaccine clinical trials.
BRAF fusions in clinically advanced non-small cell lung cancer: An emerging target for anti-BRAF therapies. (2017)

9072 Background: Although far less common than BRAF V600E base substitutions (subs) classically associated with melanomas and colorectal carcinomas, BRAF subs occur in 1-2% of non-small cell lung cancer (NSCLC). BRAF fusions are emerging treatment targets for Spitzoid melanomas and other solid tumors. The frequency of BRAF fusions and targeting potential in NSCLC has not been widely described. Methods: Hybridization capture-based comprehensive genomic profiling (CGP) was performed on 17,128 NSCLC FFPE samples sequenced to a mean coverage depth of &gt; 550X for up to 315 cancer-related genes plus 37 introns from 19 genes frequently rearranged in cancer. Genomic alterations (GA) included short variant (SV) base subs and insertions/deletions, copy number alterations, and rearrangements/fusions. Tumor mutational burden (TMB; mut/Mb) was calculated on up to 1.1 Mb of sequenced DNA. Results: BRAF fusions were identified in 42/17,128 (0.2%) NSCLC profiled. Median patient age was 67 (range 44-93 yrs). Of the BRAF fusion positive NSCLC, 55% were female. Biopsies were obtained from primary lung tumor (48%) and metastatic sites (52%). The most frequent 5’ partners were AGK, DOCK4, and TRIM24. Multiple novel BRAF fusions were identified. The genes most frequently co-altered with BRAF fusions were TP53(67%), CDKN2A(31%), EGFR (29%) and CDKN2B (26%). Overall TMB in the BRAFfusion positive cohort was low (median 3.8 mut/Mb), although 3/42 cases (7%) had &gt; 20 mut/Mb. Of the BRAF fusion driven NSCLC, 10 cases (24%) featured EGFR SV alterations. Two BRAF fusion/ EGFR SV cases featured primary exon 19 deletion and T790M mutation. Examples of BRAF fusion driven NSCLC responding to a combination of BRAFand MEK inhibitors (MEKi) will be presented. Conclusions: NSCLC BRAF fusions are a rare GA that may be associated with acquired resistance in a subset of EGFR-mutated NSCLC progressing on anti- EGFR TKI therapies. Given clinical evidence for the activity of targeted therapy approaches, molecular eligibility for clinical trials of MEKi should include these variants. The clinical evidence for responsiveness of BRAF fusion driven NSCLC provides an opportunity to personalize treatments and improve clinical outcomes for patients.