Miracle-dz/UniFAR-FTUs huggingface dataset:
Re‐orientation of the extension direction and pure extensional faulting at oblique rift margins: comparison between the Main Ethiopian Rift and laboratory experiments

In this study, we draw on a unique combination of well‐resolved fault‐slip data and earthquake focal mechanisms to constrain spatial variations in style of faulting in the obliquely extending Main Ethiopian Rift, East Africa. These data show that both boundary and internal faults – oblique and orthogonal to the plate divergence (PD) respectively – exhibit almost pure dip‐slip motion, and indicate significant local deflection in orientation of the extension direction at rift margins. Scaled analogue models closely replicate the multidisciplinary observations from the rift and suggest that the process is controlled by the presence of a deep‐seated, pre‐existing weakness – oblique to the direction of PD – that is able to cause a local rotation in the orientation of the extension direction at rift margins. Minor counterclockwise block rotations are required to accommodate the difference in slip direction along the different fault systems, as supported by existing and new palaeomagnetic data from the rift.
Shedding light on processes that control particle export and flux attenuation in the twilight zone of the open ocean

Pelagic food webs drive a flux of >10 x 1012 kg C yr−1 that exits surface waters, mostly via sinking particles through the ocean's "biological pump. " Much of this particle flux is remineralized in the poorly studied waters of the twilight zone, i.e., the layer underlying the euphotic zone and extending to 1000 m. We present a reanalysis of selected upper‐ocean studies of particulate organic carbon (POC) flux and relate these observations to a simple one‐dimensional biological model to shed light on twilight zone processes. The ecosystem model first predicts particle flux from the base of the euphotic zone, and then its attenuation below based on transformations by heterotrophic bacteria and zooplankton, and active downward transport of surface‐derived particles by zooplankton. Observations and simulations both suggest that future sampling strategies for the twilight zone should take regional variability of the euphotic zone depth (Ez) into account. In addition, conventional curvefitting of particle flux data (i.e., power law or exponential) skews our interpretation of twilight zone processes. To overcome these artifacts, we introduce two new terms: the Ez‐ratio (POC flux at Ez relative to net primary production [NPP]) and T100 (the ratio of POC flux 100 m below Ez to POC flux at Ez). A comparison of NPP, Ez‐ratios, and T100 provides a new set of metrics to classify the ocean into different regimes, representing high and low surface export and subsurface flux attenuation.
Boundary wave communication of bottom pressure and overturning changes for the North Atlantic

[1] The relationship between changes in sea-surface height, bottom pressure, and overturning is explored using isopycnal model experiments for the North Atlantic. Changes in high-latitude forcing are communicated rapidly over the basin through boundary wave propagation along the continental slope, involving a hybrid mixture of Kelvin and topographic Rossby waves, as well as spreading more slowly through advection along the western boundary. This wave communication leads to coherent signals in sea-surface height and bottom pressure variability extending for several thousand kilometers along the continental slope. The model results are in broad agreement with altimetric diagnostics, and the patterns only alter in detail with the realism of the topography. The adjustment in bottom pressure is directly linked to a change in overturning since west-east contrasts in bottom pressure are associated with a zonal integral in the meridional geostrophic flow. Correlation patterns reveal that temporal changes in overturning are primarily connected to the vertical contrast in bottom pressure, across the shelf and continental slope, along the western boundary.
Behavioral ecology of odometric memories in desert ants: acquisition, retention, and integration

Assuming that the acquisition and retention of memories have costs, properties of memories should fit the functional requirements for the system of memory. Based on a functional analysis of what path integration is meant to do, we predicted that odometric memories in desert ants should show (1) little improvement with repeated training: performance should be as good after one training trial as after six training trials, (2) decay of memory after 24 h, and (3) performance based solely on the most recent outbound trip, with no integration over multiple memories. Desert ants (Cataglyphis fortis) traveled in narrow straight plastic channels to forage for cookie crumbs in a feeder at 6- or 12-m distance. Each ant was tested once by being taken from the feeder and released 2 m from the end of a 32-m channel to run home. The distance at which the ant first turned back (first turn) constituted the data. In acquisition, groups trained one or six times before being tested had unsystematic scatter that did not differ significantly. In retention, ants tested after a 24-h delay showed larger unsystematic scatter than control animals tested after no delay. In integration, ants were trained five times at 6 or 12 m and then tested at 12 or 6 m, respectively. No evidence of integration of multiple odometric memories was found. The results show that the properties of odometric memories are indeed tailored to what the memory system is used for. Copyright 2006.
When does fishing lead to more fish? Community consequences of bottom trawl fisheries in demersal food webs

Bottom trawls are a globally used fishing gear that physically disturb the seabed and kill non-target organisms, including those that are food for the targeted fish species. There are indications that ensuing changes to the benthic invertebrate community may increase the availability of food and promote growth and even fisheries yield of target fish species. If and how this occurs is the subject of ongoing debate, with evidence both in favour and against. We model the effects of trawling on a simple ecosystem of benthivorous fish and two food populations (benthos), susceptible and resistant to trawling. We show that the ecosystem response to trawling depends on whether the abundance of benthos is top-down or bottom-up controlled. Fishing may result in higher fish abundance, higher (maximum sustainable) yield and increased persistence of fish when the benthos which is the best-quality fish food is also more resistant to trawling. These positive effects occur in bottom-up controlled systems and systems with limited impact of fish feeding on benthos, resembling bottom-up control. Fishing leads to lower yields and fish persistence in all configurations where susceptible benthos are more profitable prey. Our results highlight the importance of mechanistic ecosystem knowledge as a requirement for successful management.
Molecular Species Delimitation and Morphology of Aquatic and Sub-Aquatic Bugs (Heteroptera) in Cameroon

Aquatic and semi-aquatic bugs (Heteroptera) represent a remarkable diversity and a resurging interest has been given to documenting at the species level these insects inhabiting Cameroon in Central Africa due to their potential implication in the transmission of the bacterium Mycobacterium ulcerans, the causal agent of Buruli ulcer, an emerging human disease. A survey was carried out over two years in Cameroon. Morphological analyses were done in two steps. A first step consisted in separating the specimens based on broadly shared characters into morphotypes. The specimens were then separated into two independent batches containing each the same representation of each morphotype. One batch (309 specimens) was used by taxonomy experts on aquatic bugs for species level identification and/or to reconcile nymph with their corresponding adult species. The second batch (188 specimens) was used to define species based on the COI DNA sequences (standard sequence used for “DNA barcoding”) and using the Automatic Barcode Gap Discovery (ABGD) method. The first morphological analysis step separated the specimens into 63 different morphotypes (49 adults and 14 nymphs), which were then found to belong to 54 morphological species in the infra-orders Gerromorpha and Nepomorpha based on the species-level morphological identification, and 41–45 putative molecular species according to the gap value retained in the ABGD. Integrating morphology and “DNA barcoding” reconciled all the specimens into 62 aquatic bug species in Cameroon. Generally, we obtained a good congruence between species a priori identified based on morphology from adult morphotypes and molecular putative species. Moreover, molecular identification has allowed the association of 86% of nymphs with adults. This work illustrates the importance of integrative taxonomy.
Anti-inflammatory protein TSG-6 reduces inflammatory damage to the cornea following chemical and mechanical injury

Previous reports demonstrated that adult stem/progenitor cells from bone marrow (multipotent mesenchymal stem cells; MSCs) can repair injured tissues with little evidence of engraftment or differentiation. In exploring this phenomenon, our group has recently discovered that the therapeutic benefits of MSCs are in part explained by the cells being activated by signals from injured tissues to express an anti-inflammatory protein TNF-α–stimulated gene/protein 6 (TSG-6). Therefore, we elected to test the hypothesis that TSG-6 would have therapeutic effects in inflammatory but noninfectious diseases of the corneal surface. We produced a chemical and mechanical injury of the cornea in rats by brief application of 100% ethanol followed by mechanical debridement of corneal and limbal epithelium. Recombinant human TSG-6 or PBS solution was then injected into the anterior chamber of the eye. TSG-6 markedly decreased corneal opacity, neovascularization, and neutrophil infiltration. The levels of proinflammatory cytokines, chemokines, and matrix metalloproteinases were also decreased. The data indicated that TSG-6, a therapeutic protein produced by MSCs in response to injury signals, can protect the corneal surface from the excessive inflammatory response following injury.
LAMORE: A Stable, Scalable Approach to Latent Vector Autoregressive Modeling of Categorical Time Series

Latent vector autoregressive models for categorical time series have a wide range of potential applications from marketing research to healthcare analytics. However, a bruteforce particle filter implementation of the Expectation-Maximization (EM) algorithm often fails to estimate the maximum likelihood parameters due to the Monte Carlo approximation of the E-step and multiple local optima of the log-likelihood function. This paper proposes two auxiliary techniques that help stabilize and calibrate the estimated parameters. These two techniques, namely asymptotic mean regularization and low-resolution augmentation, do not require any additional parameter tuning, and can be implemented by modifying the brute-force EM algorithm. Experiments with simulated data show that the proposed techniques effectively stabilize the parameter estimation process. Also, experimental results using Medicare and MIMIC-II datasets illustrate various potential applications of the proposed model and methods.
Depression and Employment Status in Primary and Tertiary Care Settings

Objective: Major depressive disorder (MDD) is a leading cause of disability. Impairment in work function considerably adds to symptom burden and increases the economic impact of this disorder. Our study aimed to investigate the factors associated with work status in MDD within primary and tertiary care. Method: We used data from 2 large databases for our analysis—Study 1: the InSight database, a chart review of MDD patients treated by primary care physicians across Canada (n = 986); and Study 2: the International Mood Disorders Collaborative Project, a cross-sectional study of mood disorder patients (Canadian data only: n = 274). Results: Both studies demonstrated high rates of unemployment and disability (30.3% to 42.1%). Quebec showed the highest rate of unemployment (21%) and British Columbia had the greatest percentage of patients on disability (15%). Employed and unemployed groups were similar based on clinical characteristics; however, unemployed people may have higher age, prevalence of medical comorbidity, and greater likelihood of receiving a benzodiazepine. Increased disability rates were associated with history of childhood abuse, duration of current major depressive episode, comorbidity, benzodiazepine use, as well as greater depression and anxiety severity. The unemployed–disability groups had greater somatic symptoms and anhedonia. In keeping with this, anhedonia was the strongest predictor of disability. Absenteeism was also high across both studies. Conclusions: Unemployment and disability rates in MDD are high. The presence of anhedonia and medical comorbidity significantly influenced work status, emphasizing the need for treatment strategies to alleviate the additional symptom burden in this subpopulation.
Evidence for nonlinear coupling of planetary waves and tides in the Antarctic mesopause

Analyses of hourly-mean meridional and zonal winds near 95 km, observed with the meteor radar system at Molodezhnaya station (68°S, 45°E) during 1990, reveal the presence of long-period (2–18 day) waves with dominant periods corresponding to those of Rossby normal modes modified by mean zonal winds. Time–varying analyses indicate that although significant contributions at planetary wave periods persist with nearly constant periods for intervals of days to weeks, temporal variability of these periods is observed over longer intervals. Tidal motions, which mainly consist of the semidiurnal and the diurnal periods, demonstrate considerable modulation of their amplitudes that vary with time. The observed tidal amplitude modulations are investigated through bispectral analyses. The results of these analyses suggest nonlinear interactions of quadratic form between oscillations with periods in the range of 2 to 19 days and the diurnal and semidiurnal tides at various intervals during 1990.
On overestimation of tropical precipitation by an atmospheric GCM with prescribed SST

We investigate how an atmospheric general circulation model (AGCM) can reproduce atmospheric aspects of climate, when the boundary conditions are prescribed. The AGCM is integrated with sea surface temperature (SST) specified from an integration of a coupled general circulation model (CGCM). A systematic difference in the mean climate is found between the AGCM and the CGCM in the tropical Pacific. This difference is apparent when and where local SST is warmest. In the CGCM, precipitation does not last long due to SST and cloud‐radiation feedback. Precipitation in the AGCM, however, tends to persist longer. Results of this experiment imply that caution is needed when using an AGCM with boundary conditions derived from a CGCM for climate change studies.
Parallel Graph Mining with GPUs

Frequent graph mining is an important though computationally hard problem because it requires enumerating possibly an exponential number of candidate subgraph patterns, and checking their presence in a database of graphs. In this paper, we propose a novel approach for parallel graph mining on GPUs, which have emerged as a relatively cheap but powerful architecture for general purpose computing. However, the thread-model for GPUs is different from that of CPUs, which makes the parallelization of graph mining algorithms on GPUs a challenging task. We investigate the major challenges for GPU-based graph mining. We perform extensive experiments on several real-world and synthetic datasets, achieving speedups up to 9 over the sequential algorithm.
Supplementary Information for Mechanical Stress Inference for Two Dimensional Cell Arrays

Mechanical Stress Inference for Two Dimensional Cell Arrays Kevin K. Chiou, Lars Hufnagel, Boris I. Shraiman1,3,∗ 1 Department of Physics, University of California, Santa Barbara, CA 91306, USA. 2 Department of Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany. 3 Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 91306,USA. ∗ E-mail: shraiman@kitp.ucsb. edu
Persistent tobacco use during pregnancy and the likelihood of psychiatric disorders.

OBJECTIVES We examined the association between psychiatric disorders and tobacco use during pregnancy. METHODS Data were derived from a population-based cohort of 744 pregnant African American and White low-income women living in urban and rural areas. The Diagnostic Interview Schedule was used to assess women for 20 different psychiatric disorders. RESULTS In comparison with nonusers, persistent tobacco users (women who had used tobacco after confirmation of their pregnancy) and nonpersistent users (women who had used tobacco but not after pregnancy confirmation) were 2.5 and 2 times as likely to have a psychiatric disorder. Twenty-five percent of persistent users had at least 1 of the following diagnoses: generalized anxiety disorder, bipolar I disorder, oppositional disorder, drug abuse or dependence, and attention deficit-hyperactivity disorder. CONCLUSIONS In this cohort study, 5 diagnoses were more prevalent among persistent tobacco users than among nonusers, suggesting that several psychiatric disorders contribute to difficulty discontinuing tobacco use during pregnancy. Smoking cessation efforts focusing on pregnant women may need to address co-occurring psychiatric disorders if they are to be successful.
USE OF A LARGE-SCALE SPONTANEOUS SPEECH CORPUS IN THE STUDY OF LINGUISTIC VARIATION

Corpus of Spontaneous Japanese, or CSJ, is a large-scale database of spontaneous Japanese. It contains speech signal and transcription of about 7 million words along with various annotations like POS and phonetic labels. After describing its design issues, the potential of the CSJ as a resource for linguistic variation study was evaluated.
COMPRESSIONAL VELOCITY AND POROSITY IN SAND-CLAY MIXTURES

Laboratory measurements of porosity and compressional velocity were conducted on unconsolidated brine saturated clean Ottawa sand, pure kaolinite, and their mixtures at various confining pressures. A peak in P velocity versus clay content in unconsolidated sand‐clay mixtures at 40 percent clay by weight was found. The peak in velocity is 20–30 percent higher than for either pure clay or clean sand. A minimum in porosity versus clay content at 20–40 percent clay by weight is also observed. Such behavior is explained using a micro‐geometrical model for mixtures of sand and clay in which two classes of sediments are considered: (1) sands and shaley sands, in which clay is dispersed in the pore space of load bearing sand and thus reduces porosity and increases the elastic moduli of the pore‐filling material and (2) shales and sandy shales, in which sand grains are dispersed in a clay matrix. For these sediments, the model reproduces the extrema in velocity and porosity and accounts for much of the scatter in .
A double-blind comparative study of clozapine and risperidone in the management of severe chronic schizophrenia.

OBJECTIVE This prospective, double-blind, multicenter, parallel-group study compared the efficacy and safety of therapeutic doses of clozapine and risperidone in patients with severe chronic schizophrenia and poor previous treatment response. METHOD Male or female patients aged 18-65 years who met DSM-IV criteria for schizophrenia and study requirements for poor previous treatment response (N=273) were randomly assigned to double-blind treatment with either clozapine or risperidone administered over 12 weeks in increasing increments. The primary efficacy measures were the magnitude of improvement in Brief Psychiatric Rating Scale (BPRS) and Clinical Global Impression (CGI) scores. Adverse events were recorded throughout the study. RESULTS The magnitude of improvement in mean BPRS and CGI scores from baseline to end of the study was significantly greater in the clozapine group than in the risperidone group. Statistically significant differences in favor of clozapine were also seen for most of the secondary efficacy measures (Positive and Negative Syndrome Scale, Calgary Depression Scale, Psychotic Depression Scale, and Psychotic Anxiety Scale). The adverse event profile was similar for both treatment groups, with a lower risk of extrapyramidal symptoms in the clozapine group. CONCLUSIONS Clozapine showed superior efficacy over risperidone in this patient population. Both treatments were equally well tolerated as demonstrated through their adverse event profiles, although as expected clozapine was associated with a lower risk of extrapyramidal symptoms than risperidone.
Positive and Negative Cognate Amino Acid Bias Affects Compositions of Aminoacyl-tRNA Synthetases and Reflects Functional Constraints on Protein Structure

By comparing phylogenetically related tRNA syn- thetases (enzymes that specifically aminoacylate tRNAs), a controlled natural experiment can reveal synthetases' coevolution with their cognate amino acid substrate. Analyses of metabolic cost minimi- zation confirm the existence of cognate avoidance in tRNA synthetase compositions. It is found that cognate avoidance increases and decreases, respectively, with proteomic amino acid usage in Escherichia coli and Bacillus subtilis.
LMA and sterile neutrinos: a case for resonance spin flavour precession?

Open questions remain after the confirmation of LMA as the dominant solution to the solar neutrino deficit. These are the apparent time modulation of the solar neutrino event rates in the Homestake, Gallium and SuperKamiokande experiments, possibly related to solar magnetic activity, the discrepancy between the event rate in the Homestake experiment and its theoretical prediction and the absence of the electron spectrum upturn in SuperKamiokande at energies below 6-8 MeV. We search for a possible understanding of these questions in the context of resonant spin flavour precession to sterile neutrinos, assuming a class of magnetic field profiles anchored in the upper radiation/lower convection zone. We consider the simplest such model beyond the standard 2ν flavour LMA one, with one single magnetic moment transition between active and sterile state and vanishing vacuum mixing. The preferred mass square difference is Δm210 = O(10−8 eV2). The Ga rate appears to be the most sensitive of all to solar activity. It is also found that a field profile extending within a longer region in the radial direction is favoured over another with a shorter span, and leads to a stronger suppression than in the LMA case of the intermediate energy neutrinos and some of the 8B ones.