gebhart/patrepeval huggingface dataset:
Challenges in Including BCA in Planning Approval Processes: Coal Mine Projects in New South Wales, Australia (2015)

A requirement for project proponents to include a benefit-cost analysis (BCA) as a component of their environmental impact assessments is implied in planning approval legislation in New South Wales, Australia. Fulfilling that requirement in the context of three large-scale expansions of coal mines has led to the application of choice modeling to estimate values for the main environmental, social, and heritage impacts. A number of particular issues have emerged in those applications: the framing of choice sets so that incentive-compatible willingness-to-pay questions are asked; the inclusion of “existence values” associated with employment opportunities provided by mines; and the incorporation of environmental offsets as part of the choice task given to respondents. The benefit-cost analyses of the coal mining projects have proven controversial. While the government agency responsible for administering the project approval process has used them as an input to decision-making, in some cases its recommendations have been “over-ridden” by the imposition of subjectively determined administrative rules. In one case, an appeal through legal channels against an approval was successful in part because the judge who heard the appeal dismissed the BCA findings because it was contrary to his own viewpoint of the merits of the case. In response, the state government has introduced legislation that requires greater “weight” to be given to the development benefits of coal mining. These responses have left the role of BCA and nonmarket valuation in the decision-making process in “limbo,” with practitioners and policy makers unsure as to the future of the methods in politically charged contexts.
Search for long-lived, massive particles in events with a displaced vertex and a muon with large impact parameter in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>p</mml:mi><mml:mi>p</mml:mi></mml:math> collisions at <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msqrt><mml:mi>s</mml:mi></mml:msqrt><mml:mo>=</mml:mo><mml:mn>13</mml:mn><mml:mtext> </mml:mtext><mml:mtext> </mml:mtext><mml:mi>TeV</mml:mi></mml:math> with the ATLAS detector (2020)

A search for long-lived particles decaying into hadrons and at least one muon is presented. The analysis selects events that pass a muon or missing-transverse-momentum trigger and contain a displaced muon track and a displaced vertex. The analyzed dataset of proton-proton collisions at $\sqrt{s}=13\text{ }\text{ }\mathrm{TeV}$ was collected with the ATLAS detector and corresponds to $136\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$. The search employs dedicated reconstruction techniques that significantly increase the sensitivity to long-lived particle decays that occur in the ATLAS inner detector. Background estimates for Standard Model processes and instrumental effects are extracted from data. The observed event yields are compatible with those expected from background processes. The results are presented as limits at 95% confidence level on model-independent cross sections for processes beyond the Standard Model, and interpreted as exclusion limits in scenarios with pair production of long-lived top squarks that decay via a small $R$-parity-violating coupling into a quark and a muon. Top squarks with masses up to 1.7 TeV are excluded for a lifetime of 0.1 ns, and masses below 1.3 TeV are excluded for lifetimes between 0.01 ns and 30 ns.
Reconfigurable MRI coil technology can substantially reduce RF heating at the tips of bilateral deep brain stimulation implants (2018)

Abstract Patients with deep brain stimulation (DBS) implants can significantly benefit from magnetic resonance imaging (MRI) examination, however, access to MRI is restricted in this patients because of safety concerns due to RF heating of the leads. Recently we introduced a patient-adjustable reconfigurable MRI coil system to reduce the SAR at the tip of deep brain stimulation implants during MRI at 1.5T. A simulation study with realistic models of single (unilateral) DBS leads demonstrated a substantial reduction in the local SAR up to 500-fold could be achieved using the coil system compared to quadrature birdcage coils. Many patients however, have bilateral DBS implants and the question arises whether the rotating coil system can be used in for them. This work reports the results of phantom experiments measuring the temperature rise at the tips of bilateral DBS implants with realistic trajectories extracted from postoperative CT images of 10 patients (20 leads in total). A total of 200 measurements were performed to record temperature rise at the tips of the leads during 2 minutes of scanning with the coil rotated to cover all accessible rotation angles. In all patients, we were able to find an optimum coil rotation angle and reduced the heating of both left and right leads to a level below the heating produced by the body coil. An average heat reduction of 65% was achieved for bilateral leads. Reconfigurable coil technology introduces a promising approach for imaging of patients with DBS implants.
Hybrid input spaces for exemplar-based noise robust speech recognition using coupled dictionaries (2015)

Exemplar-based feature enhancement successfully exploits a wide temporal signal context. We extend this technique with hybrid input spaces that are chosen for a more effective separation of speech from background noise. This work investigates the use of two different hybrid input spaces which are formed by incorporating the full-resolution and modulation envelope spectral representations with the Mel features. A coupled output dictionary containing Mel exemplars, which are jointly extracted with the hybrid space exemplars, is used to reconstruct the enhanced Mel features for the ASR back-end. When compared to the system which uses Mel features only as input exemplars, these hybrid input spaces are found to yield improved word error rates on the AURORA-2 database especially with unseen noise cases.
Polarization dependence of transient photoconductivity in<i>trans</i>-polyacetylene (1987)

We present the results of a series of measurements of the polarization dependence of the transient photoconductive response in both oriented and nonoriented trans-polyacetylene. Our results indicate that in nonoriented samples, the short-time photoconductivity is dominated by intrachain absorption and intrachain transport, while in oriented samples both interchain and intrachain photogeneration (with different absorption depths) of charge carriers are important. In oriented samples the photoconduction due to interchain excitation is slightly larger than that due to intrachain excitation.
EBF1 promotes triple-negative breast cancer progression by surveillance of the HIF1α pathway (2022)

Early B cell factor 1 (EBF1) is a transcriptional factor with a variety of roles in cell differentiation and metabolism. However, the functional roles of EBF1 in tumorigenesis remain elusive. Here, we demonstrate that EBF1 is highly expressed in triple-negative breast cancer (TNBC). Furthermore, EBF1 has a pivotal role in the tumorigenicity and progression of TNBC. Moreover, we found that depletion of EBF1 induces extensive cell mitophagy and inhibits tumor growth. Genome-wide mapping of the EBF1 transcriptional regulatory network revealed that EBF1 drives TNBC tumorigenicity by assembling a transcriptional complex with HIF1α that fine-tunes the expression of HIF1α targets via suppression of p300 activity. EBF1 therefore holds HIF1α activity in check to avert extensive mitophagy-induced cell death. Our findings reveal a key function for EBF1 as a master regulator of mitochondria homeostasis in TNBC and indicate that targeting this pathway may offer alternative treatment strategies for this aggressive subtype of breast cancer.
Large-Scale Functionalized Metasurface-Based SARS-CoV-2 Detection and Quantification (2022)

Plasmonic metasurfaces consist of metal-dielectric interfaces that are excitable at background and leakage resonant modes. The sharp and plasmonic excitation profile of metal-free electrons on metasurfaces at the nanoscale can be used for practical applications in diverse fields, including optoelectronics, energy harvesting, and biosensing. Currently, Fano resonant metasurface fabrication processes for biosensor applications are costly, need clean room access, and involve limited small-scale surface areas that are not easy for accurate sample placement. Here, we leverage the large-scale active area with uniform surface patterns present on optical disc-based metasurfaces as a cost-effective method to excite asymmetric plasmonic modes, enabling tunable optical Fano resonance interfacing with a microfluidic channel for multiple target detection in the visible wavelength range. We engineered plasmonic metasurfaces for biosensing through efficient layer-by-layer surface functionalization toward real-time measurement of target binding at the molecular scale. Further, we demonstrated the quantitative detection of antibodies, proteins, and the whole viral particles of SARS-CoV-2 with a high sensitivity and specificity, even distinguishing it from similar RNA viruses such as influenza and MERS. This cost-effective plasmonic metasurface platform offers a small-scale light-manipulation system, presenting considerable potential for fast, real-time detection of SARS-CoV-2 and pathogens in resource-limited settings.
ChemInform Abstract: Thienospirans. Part 5. Thienospirans via Directed Lithiations. (1988)

Abstract Lithiation of 3‐bromothiophene (II) followed by reaction with benzaldehyde (IIIa) or carbon dioxide (IIIb) produces the adducts (IV).
Development of human white matter pathways in utero over the second and third trimester (2021)

During the second and third trimesters of human gestation, rapid neurodevelopment is underpinned by fundamental processes including neuronal migration, cellular organization, cortical layering, and myelination. In this time, white matter growth and maturation lay the foundation for an efficient network of structural connections. Detailed knowledge about this developmental trajectory in the healthy human fetal brain is limited, in part, due to the inherent challenges of acquiring high-quality MRI data from this population. Here, we use state-of-the-art high-resolution multishell motion-corrected diffusion-weighted MRI (dMRI), collected as part of the developing Human Connectome Project (dHCP), to characterize the in utero maturation of white matter microstructure in 113 fetuses aged 22 to 37 wk gestation. We define five major white matter bundles and characterize their microstructural features using both traditional diffusion tensor and multishell multitissue models. We found unique maturational trends in thalamocortical fibers compared with association tracts and identified different maturational trends within specific sections of the corpus callosum. While linear maturational increases in fractional anisotropy were seen in the splenium of the corpus callosum, complex nonlinear trends were seen in the majority of other white matter tracts, with an initial decrease in fractional anisotropy in early gestation followed by a later increase. The latter is of particular interest as it differs markedly from the trends previously described in ex utero preterm infants, suggesting that this normative fetal data can provide significant insights into the abnormalities in connectivity which underlie the neurodevelopmental impairments associated with preterm birth.
Finding Kinship in the Women in Radio Science Chapter [Women in Engineering] (2022)

This article introduces the Women in Radio Science (WIRS) Chapter of the U.S. National Committee (USNC) of the International Union of Radio Science (URSI). The unique challenges of minority groups in the radio science community are discussed. The value and impact of diversifying the scientific workplace are argued, and the promise of a women-led radio science community is presented.
Pleiotropy of systemic lupus erythematosus risk alleles and cardiometabolic disorders: A phenome-wide association study and inverse-variance weighted meta-analysis (2021)

A weighted GRS for SLE was associated with an increased risk of several autoimmune-related phenotypes including type I diabetes but not with cardiometabolic disorders.
Integrated lipidomics and proteomics network analysis highlights lipid and immunity pathways associated with Alzheimer’s disease (2020)

Abstract INTRODUCTION There is an urgent need to understand the molecular mechanisms underlying Alzheimer’s Disease (AD) to enable early diagnosis and develop effective treatments. Here we aim to investigate Alzheimer’s dementia using an unsupervised lipid, protein and gene multi-omic integrative approach. METHODS A lipidomics dataset (185 AD, 40 MCI and 185 controls) and a proteomics dataset (201 AD patients, 104 MCI individuals and 97 controls) were utilised for weighted gene co-expression network analyses (WGCNA). An additional proteomics dataset (94 AD, 55 MCI and 100 controls) was included for external proteomics validation. Modules created within each modality were correlated with clinical AD diagnosis, brain atrophy measures and disease progression, as well as with each other. Gene Ontology (GO) enrichment analysis was employed to examine the biological processes and molecular and cellular functions for protein modules associated with AD phenotypes. Lipid species were annotated in the lipid modules associated with AD phenotypes. Associations between established AD risk loci and lipid/protein modules that showed high correlation with AD phenotypes were also explored. RESULTS Five of the 20 identified lipid modules and five of the 17 identified protein modules were correlated with AD phenotypes. Lipid modules comprising of phospholipids, triglycerides, sphingolipids and cholesterol esters, correlated with AD risk loci involved in immune response and lipid metabolism. Five protein modules involved in positive regulation of cytokine production, neutrophil mediated immunity, humoral immune responses were correlated with AD risk loci involved in immune and complement systems. DISCUSSION We have shown the first multi-omic study linking genes, proteins and lipids to study pathway dysregulation in AD. Results identified modules of tightly regulated lipids and proteins that were strongly associated with AD phenotypes and could be pathology drivers in lipid homeostasis and innate immunity. Research in Context Lipid and protein modules were preserved amongst Alzheimer’s disease (AD) patients, participants with mild cognitive impairment (MCI) and controls. Protein modules were also externally validated. Five lipid and five protein modules out of a total of thirty-seven correlated with clinical AD diagnosis, brain atrophy measurements and the rate of cognitive decline in AD. Lipid and protein modules associated with AD phenotypes showed associations with established AD risk loci involved in lipid and immune pathways.
Infantile Pompe Disease: Clinical and Genetic Characteristics With an Experience of Enzyme Replacement Therapy (2011)

Pompe disease is an autosomal recessive disorder caused by lysosomal acid α-glucosidase deficiency. Infantile-onset Pompe disease presents with cardiomyopathy and hypotonia, leading to premature death. This article describes 7 infantile Pompe disease cases and provides their molecular bases and clinical outcomes after enzyme replacement therapy for the first time in Korea. Molecular genetic analyses revealed the presence of 9 different mutations, including 5 novel mutations (c.2171C>A, c.2774C>T, c.1582_3de12, c.1261_1263Tms, and c.1322_1326+9de114). The most common mutation in these 7 patients was c.1316T>A (28%). Four patients received intravenous recombinant human acid α-glucosidase therapy for 2 years, on average, without significant side effects during the treatment course. They all exhibited increased muscle power, with considerable improvement in cardiac function. Pompe disease is heterogeneous regarding both clinical features and molecular characteristics. Early identification of Pompe disease is very important, considering that enzyme replacement therapy is a safe and effective treatment for early-onset patients.
Simulation of a Strategy for the Assessment of Damage in Human Bones by Using FEM and Signal Processing (2011)

The aim of this work is to propose a non-invasive technique aimed at assessing the evolution of damage in elongated bones that could be caused, for instance, by metabolic diseases. The technique exploits signals related to mechanical guided waves traveling along the bone to characterize its mechanical properties in a total non-destructive manner. Such properties can be used as an indicator of the damage level present in the bone. The preliminary results motivate future studies
Metagenomic and Metatranscriptomic Insights into Population Diversity of <i>Microcystis</i> Blooms: Spatial and Temporal Dynamics of <i>mcy</i> Genotypes, Including a Partial Operon That Can Be Abundant and Expressed (2022)

Cyanobacterial harmful algal blooms (cyanoHABs) degrade freshwater ecosystems globally. Microcystis aeruginosa often dominates cyanoHABs and produces microcystin (MC), a class of hepatotoxins that poses threats to human and animal health. Microcystin toxicity is influenced by distinct structural elements across a diversity of related molecules encoded by variant <i>mcy</i> operons. However, the composition and distribution of <i>mcy</i> operon variants in natural blooms remain poorly understood. Here, we characterized the variant composition of <i>mcy</i> genes in western Lake Erie <i>Microcystis</i> blooms from 2014 and 2018. Sampling was conducted across several spatial and temporal scales, including different bloom phases within 2014, extensive spatial coverage on the same day (2018), and frequent, autonomous sampling over a 2-week period (2018). Mapping of metagenomic and metatranscriptomic sequences to reference sequences revealed three <i>Microcystis mcy</i> genotypes: complete (all genes present [<i>mcyA-J</i>]), partial (truncated <i>mcyA</i>, complete <i>mcyBC</i>, and missing <i>mcyD-J</i>), and absent (no <i>mcy</i> genes). We also detected two different variants of <i>mcyB</i> that may influence the production of microcystin congeners. The relative abundance of these genotypes was correlated with pH and nitrate concentrations. Metatranscriptomic analysis revealed that partial operons were, at times, the most abundant genotype and expressed <i>in situ</i>, suggesting the potential biosynthesis of truncated products. Quantification of genetic divergence between genotypes suggests that the observed strains are the result of preexisting heterogeneity rather than <i>de novo</i> mutation during the sampling period. Overall, our results show that natural <i>Microcystis</i> populations contain several cooccurring <i>mcy</i> genotypes that dynamically shift in abundance spatiotemporally via strain succession and likely influence the observed diversity of the produced congeners. <b>IMPORTANCE</b> Cyanobacteria are responsible for producing microcystins (MCs), a class of potent and structurally diverse toxins, in freshwater systems around the world. While microcystins have been studied for over 50 years, the diversity of their chemical forms and how this variation is encoded at the genetic level remain poorly understood, especially within natural populations of cyanobacterial harmful algal blooms (cyanoHABs). Here, we leverage community DNA and RNA sequences to track shifts in <i>mcy</i> genes responsible for producing microcystin, uncovering the relative abundance, expression, and variation of these genes. We studied this phenomenon in western Lake Erie, which suffers annually from cyanoHAB events, with impacts on drinking water, recreation, tourism, and commercial fishing.
Design and Characterization of Heteroleptic Ruthenium Complexes Containing Benzimidazole Ligands for Dye-Sensitized Solar Cells: The Effect of Thiophene and Alkyl Substituents on Photovoltaic Performance (2013)

We designed heteroleptic ruthenium complexes RD16–RD18 containing fluoro-substituted and thiophene-based benzimidazole ligands for dye-sensitized solar cells. Whereas the substitution of only fluorine in the RD12 device has an effect of enhancing the open-circuit voltage (VOC), additional substitution of thiophene in the RD16–RD18 sensitizers showed a slightly decreased VOC. Systematic enhanced short-circuit current density (JSC) and efficiency (η) of power conversion of the devices had the order RD18 > RD17 > RD16 > RD12 > N719, attributed to the increasing light-harvesting ability and the broadened spectral features with thiophene-based ligands. Measurements of charge extraction and intensity-modulated photovoltage spectra indicate that thiophene substitution shifts downward the TiO2 potential and accelerates charge recombination, but inclusion of a long hexyl chain on the thiophene moiety retards charge recombination to account for the variation of VOC in the series. For a duration test of device performance at ambient temperature, only ∼2% degradation of cell performance was found for the devices of RD18 and RD12 over 2000 h, but a 10% decrease in overall efficiency was observed in the N719 device.
New hardness results for congestion minimization and machine scheduling (2004)

We study the approximability of two natural NP-hard problems. The first problem is congestion minimization in directed networks. We are given a directed capacitated graph and a set of source-sink pairs. The goal is to route all pairs with minimum congestion on the network edges. A special well-studied case of this problem is the edge-disjoint paths problem, where all edges have unit capacities. The second problem is discrete machine scheduling, where we are given a set of jobs, and for each job a list of intervals in which it can be scheduled. The goal is to find the smallest number of machines on which all jobs can be scheduled, such that no two jobs assigned to the same machine overlap. Both problems are known to be O(log n/log log n)-approximable via the randomized rounding technique of Raghavan and Thompson. However, until recently, only a Max SNP hardness was known for each problem. We make some progress in closing this gap by showing that both problem are Ω(log log n)-hard to approximate unless NP ⊆ DTIME(nO(log log log n)). Our hardness proof for congestion minimization holds even for the special case of the edge-disjoint paths problem.
A robust omics-based approach for the identification of glucosinolate biosynthetic genes (2008)

Transcriptome coexpression analysis, which is based on a vast amount of transcriptome data obtained by using DNA arrays, has become a routine method for functional genomics studies in Arabidopsis. This analysis enables us to predict the function of genes on the basis of a simple assumption that a set of genes involved in a particular biological process can be coexpressed under the control of a shared regulatory system. Candidate genes involved in glucosinolate biosynthesis were successfully identified by this approach. In this review, the methodology of coexpression analysis is briefly described. The advantages and disadvantages of this analysis are also discussed in the context of its ability to predict gene functions involved in glucosinolate biosynthesis.