Miracle-dz/UniFAR-FTUs huggingface dataset:
Linear and Nonlinear Hydrological Cycle Responses to Increasing Sea Surface Temperature

An effective mechanism for determining tropical rainfall patterns in response to sea surface temperature (SST) increases with varying magnitude and horizontal distribution has not been developed thus far in climate change studies. In order to examine changes in precipitation pattern with increasing SST, we conducted a series of atmospheric general circulation model experiments using a 30 year record of observed SST for which either globally uniform SST increases of 1 K, 2 K, and 4 K or El Niño/La Niña‐like patterned SST anomaly has been imposed. Although the global‐mean precipitation linearly increases with the SST increase irrespective of its spatial distribution, regional precipitation changes were found to occur nonlinearly depending on the magnitude of the uniform SST increase. Owing to nonlinearity in the atmospheric circulation response, the regional hydrological sensitivity was larger with a smaller increase in SST. The precipitation response to the SST pattern was, however, quasi‐linear to the magnitude of the SST change and can be separated from the response to the uniform SST increase. This study thus emphasizes the importance of relative amplitudes of uniform and structured SST increases for future rainfall projection.
Cholinergic optimization of cue‐evoked parietal activity during challenged attentional performance

The detection of salient or instrumental stimuli and the selection of cue‐evoked responses are mediated by a fronto‐parietal network that is modulated by cholinergic inputs originating from the basal forebrain. Visual cues that guide behavior are more strongly represented in the posterior parietal cortex (PPC) than are similar cues that are missed or task‐irrelevant. Although the crucial role of cholinergic inputs in cue detection has been demonstrated by lesion studies, the role of PPC neurons in the cholinergic modulation of cue detection is unclear. We recorded extracellular spikes from PPC neurons of rats performing a sustained attention task, before and after selective removal of cholinergic inputs to the recording site. Visual cues that were subsequently detected evoked significant increases in the PPC firing rate. In the absence of cholinergic input, the activation of PPC neurons by detected cues was greatly diminished. When a visual distractor was introduced during task performance, a population of PPC neurons selectively responded to the distractor. As a result of cholinergic deafferentation, distractor‐related neuronal activity was enhanced, and the detection‐related activity was further suppressed. Thus, in deafferented subjects, the distractor lowered the signal‐to‐noise ratio of cue‐evoked responses. This impairment in cue‐evoked neuronal activity may have mediated the increased response latencies observed for detected cues in the presence of the distractor. Additional experiments demonstrated that the effects of cholinergic deafferentation were not confounded by extended practice or electrode depth. Collectively, these findings indicate that cholinergic inputs to PPC neurons amplify cue detection, and may also act to suppress irrelevant distractors.
Selecting Informative Universum Sample for Semi-Supervised Learning

The Universum sample, which is defined as the sample that doesn't belong to any of the classes the learning task concerns, has been proved to be helpful in both supervised and semi-supervised settings. The former works treat the Universum samples equally. Our research found that not all the Universum samples are helpful, and we propose a method to pick the informative ones, i.e., in-between Universum samples. We also set up a new semi-supervised framework to incorporate the in-between Universum samples. Empirical experiments show that our method outperforms the former ones.
Computerized system to enhance the clinical diagnosis of pigmented cutaneous malignancies

Background An increase in the incidence of cutaneous malignant melanoma in recent years has not been accompanied by satisfactory progress in diagnostic methods. This study was carried out to evaluate a specially designed computerized image analysis system, called Derma Vision, to aid in the differentiation between malignant and benign cutaneous pigmented lesions.
Sketch classification and classification-driven analysis using Fisher vectors

We introduce an approach for sketch classification based on Fisher vectors that significantly outperforms existing techniques. For the TU-Berlin sketch benchmark [Eitz et al. 2012a], our recognition rate is close to human performance on the same task. Motivated by these results, we propose a different benchmark for the evaluation of sketch classification algorithms. Our key idea is that the relevant aspect when recognizing a sketch is not the intention of the person who made the drawing, but the information that was effectively expressed. We modify the original benchmark to capture this concept more precisely and, as such, to provide a more adequate tool for the evaluation of sketch classification techniques. Finally, we perform a classification-driven analysis which is able to recover semantic aspects of the individual sketches, such as the quality of the drawing and the importance of each part of the sketch for the recognition.
Prevalence of Acute Coronary Syndrome in Patients Suspected for Pulmonary Embolism or Acute Aortic Syndrome: Rationale for the Triple Rule-Out Concept

Background The aims of the study were to evaluate the prevalence of acute coronary syndrome (ACS) among patients presenting with atypical chest pain who are evaluated for acute aortic syndrome (AAS) or pulmonary embolism (PE) with computed tomoangiography (CTA) and discuss the rationale for the use of triple rule-out (TRO) protocol for triaging these patients. Methods This study is a retrospective analysis of patients presenting with atypical chest pain and evaluated with thoracic (CTA), for suspicion of AAS/PE. Two physicians reviewed patient files for demographic characteristics, initial CT and final clinical diagnosis. Patients were classified according to CTA finding into AAS, PE and other diagnoses and according to final clinical diagnosis into AAS, PE, ACS and other diagnoses. Results Four hundred and sixty-seven patients were evaluated: 396 (84.8%) patients for clinical suspicion of PE and 71 (15.2%) patients for suspicion of AAS. The prevalence of ACS and AAS was low among the PE patients: 5.5% and 0.5% respectively (P = 0.0001), while the prevalence of ACS and PE was 18.3% and 5.6% among AAS patients (P = 0.14 and P = 0.34 respectively). Conclusion The prevalence of ACS and AAS among patients suspected clinically of having PE is limited while the prevalence of ACS and PE among patients suspected clinically of having AAS is significant. Accordingly patients suspected for PE could be evaluated with dedicated PE CTA while those suspected for AAS should still be triaged using TRO protocol.
Submodular Optimization under Noise

We consider the problem of maximizing a monotone submodular function under noise. There has been a great deal of work on optimization of submodular functions under various constraints, resulting in algorithms that provide desirable approximation guarantees. In many applications, however, we do not have access to the submodular function we aim to optimize, but rather to some erroneous or noisy version of it. This raises the question of whether provable guarantees are obtainable in presence of error and noise. We provide initial answers, by focusing on the question of maximizing a monotone submodular function under a cardinality constraint when given access to a noisy oracle of the function. We show that: - For a cardinality constraint $k \geq 2$, there is an approximation algorithm whose approximation ratio is arbitrarily close to $1-1/e$; - For $k=1$ there is an algorithm whose approximation ratio is arbitrarily close to $1/2$. No randomized algorithm can obtain an approximation ratio better than $1/2+o(1)$; -If the noise is adversarial, no non-trivial approximation guarantee can be obtained.
Empirical Evidence on Inflation Expectations in the New Keynesian Phillips Curve

We review the main identification strategies and empirical evidence on the role of expectations in the New Keynesian Phillips curve, paying particular attention to the issue of weak identification. Our goal is to provide a clear understanding of the role of expectations that integrates across the different papers and specifications in the literature. We discuss the properties of the various limited-information econometric methods used in the literature and provide explanations of why they produce conflicting results. Using a common dataset and a flexible empirical approach, we find that researchers are faced with substantial specification uncertainty, as different combinations of various a priori reasonable specification choices give rise to a vast set of point estimates. Moreover, given a specification, estimation is subject to considerable sampling uncertainty due to weak identification. We highlight the assumptions that seem to matter most for identification and the configuration of point estimates. We conclude that the literature has reached a limit on how much can be learned about the New Keynesian Phillips curve from aggregate macroeconomic time series. New identification approaches and new datasets are needed to reach an empirical consensus.
New interglacial deposits from Copenhagen, Denmark: marine Isotope Stage 7

During a pre‐site survey and construction of a new metro route and station in Copenhagen, fossiliferous organic‐rich sediments were encountered. This paper reports on multidisciplinary investigations of these organic sediments, which occurred beneath a sediment succession with a lower till, glacifluvial sand and gravel, an upper till and glacifluvial sand. The organic sediments were underlain by glacifluvial sand and gravel. The organic‐rich sediments, which were up to 0.5 m thick, accumulated in a low‐energy environment, possibly an oxbow lake. They were rich in plant fossils, which included warmth‐demanding trees and other species, such as Najas minor, indicating slightly higher summer temperatures than at present. Freshwater shells were also frequent. Bithynia opercula allowed the sediments to be put into an aminostratigraphical framework. The amino acid racemization (AAR) ratios indicate that the organic sediments formed during Marine Isotope Stage 7 (MIS 7), which is consistent with optically stimulated luminescence dating that gave ages of 206 and 248 ka from the underlying minerogenic deposit. The assemblages from Trianglen are similar to interglacial deposits from the former Free Port (1.4 km away) in Copenhagen, except that Corbicula and Pisidium clessini were not found at Trianglen. The presence of these bivalves at the Free Port and the ostracod Scottia tumida at Trianglen indicates a pre‐Eemian age. AAR data from archived Bithynia opercula from the Free Port were almost identical to those from Trianglen, indicating that the two sites are contemporary. We suggest the Trianglen interglacial be used as a local name for the MIS 7 interglacial deposits in Copenhagen. MIS 7 deposits have rarely been documented from the region, but MIS 7 deposits may have been mistaken for other ages. The use of AAR ratios in Bithynia opercula has a great potential for correlation of interglacial non‐marine deposits in mainland northern Europe.
The dynamic three-dimensional organization of the diploid yeast genome

The budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes. Even in this well-studied model, it is unclear how homolog pairing in diploids and environment-induced gene relocalization influence overall genome organization. Here, we performed high-throughput chromosome conformation capture on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid yeasts. After controlling for the Rabl-like orientation, we observe significant homolog proximity that increased in saturated culture conditions. Surprisingly, we observe a localized increase in homologous interactions between the HAS1 alleles specifically under galactose induction and saturated growth, mediated by association with nuclear pore complexes at the nuclear periphery. Together, these results reveal that the diploid yeast genome has a dynamic and complex 3D organization.
Starting together, growing apart: gender gaps in learning from preschool to adulthood in four developing countries

This paper studies gender gaps in multiple learning domains – quantitative skills, vocabulary and reading – for children from the age of 5 to 19 years of age using unique panel data from Ethiopia, India, Peru and Vietnam on two cohorts of children with linked test scores and detailed household-based information. In all countries, both for math and receptive vocabulary, we find that there are no gender gaps prior to school entry (5 years); these gaps emerge later, widening particularly between the ages of 12 and 15 years, favouring boys in Ethiopia and India and favouring girls in Vietnam; subsequently, these learning gaps appear to mostly persist until early adulthood. Our analysis, both cross-sectional and over time, pays special attention to issues arising from selective enrolment, from the ordinality of test outcomes, and from the issue of decay in test scores. Finally, we investigate the sources of divergence between 12-15 years using panel-based value-added models with a rich set of covariates including past achievement, child health, time use, parental education and wealth, and the quality of schooling. In our most extensive specifications, we can explain between half and two-thirds of the cross-sectional gender gap in test scores but a substantial unexplained portion remains. To the best of our knowledge, this is the most extensive comparable panel-based investigation of this question over a long age range, covering multiple countries and test domains, and with extensive background information to enable an investigation of the sources of observed gaps. ⇤Preliminary draft, for comments only. Please do not cite or circulate without permission of the authors. We thank Sonia Bhalotra, Doug Gollin, Krzystof Karbownik, Diane Schenzenbach and seminar participants at the University of Oxford, the APPAM International Conference (LSE) and Friedrich Alexander University, Nuremberg for helpful comments. This project is based on data from the Young Lives study which is core-funded by UK aid from the Department for International Development and was co-funded from 2010 to 2014 by the Netherlands Ministry of Foreign Affairs.
Hybrid checkpointing using emerging nonvolatile memories for future exascale systems

The scalability of future Massively Parallel Processing (MPP) systems is being severely challenged by high failure rates. Current centralized Hard Disk Drive (HDD) checkpointing results in overhead of 25% or more at petascale. Since systems become more vulnerable as the node count keeps increasing, novel techniques that enable fast and frequent checkpointing are critical to the future exascale system implementation. In this work, we first introduce one of the emerging nonvolatile memory technologies, Phase-Change Random Access Memory (PCRAM), as a proper candidate of the fast checkpointing device. After a thorough analysis of MPP systems, failure rates and failure sources, we propose a PCRAM-based hybrid local/global checkpointing mechanism which not only provides a faster checkpoint storage, but also boosts the effectiveness of other orthogonal techniques such as incremental checkpointing and background checkpointing. Three variant implementations of the PCRAM-based hybrid checkpointing are designed to be adopted at different stages and to offer a smooth transition from the conventional in-disk checkpointing to the instant in-memory approach. Analyzing the overhead by using a hybrid checkpointing performance model, we show the proposed approach only incurs less than 3% performance overhead on a projected exascale system.
Cortical sources of the early components of the visual evoked potential

This study aimed to characterize the neural generators of the early components of the visual evoked potential (VEP) to isoluminant checkerboard stimuli. Multichannel scalp recordings, retinotopic mapping and dipole modeling techniques were used to estimate the locations of the cortical sources giving rise to the early C1, P1, and N1 components. Dipole locations were matched to anatomical brain regions visualized in structural magnetic resonance imaging (MRI) and to functional MRI (fMRI) activations elicited by the same stimuli. These converging methods confirmed previous reports that the C1 component (onset latency 55 msec; peak latency 90–92 msec) was generated in the primary visual area (striate cortex; area 17). The early phase of the P1 component (onset latency 72–80 msec; peak latency 98–110 msec) was localized to sources in dorsal extrastriate cortex of the middle occipital gyrus, while the late phase of the P1 component (onset latency 110–120 msec; peak latency 136–146 msec) was localized to ventral extrastriate cortex of the fusiform gyrus. Among the N1 subcomponents, the posterior N150 could be accounted for by the same dipolar source as the early P1, while the anterior N155 was localized to a deep source in the parietal lobe. These findings clarify the anatomical origin of these VEP components, which have been studied extensively in relation to visual‐perceptual processes. Hum. Brain Mapping 15:95–111, 2001. © 2001 Wiley‐Liss, Inc.
The reinforcing properties of salsolinol in the ventral tegmental area: evidence for regional heterogeneity and the involvement of serotonin and dopamine.

BACKGROUND Salsolinol (SAL), the condensation product of acetaldehyde and dopamine, may be a factor contributing to alcohol abuse. Previous research indicated that both ethanol and acetaldehyde are self-administered into the posterior ventral tegmental area (VTA). The current study examined SAL self-infusions into the VTA, and determined the involvement of dopamine neurons and 5-HT3 receptors in this process. METHODS The intracranial self-administration technique was used to determine the self-infusion of SAL into the VTA of adult, male Wistar rats. The rats were placed in 2-lever (active and inactive) experimental chambers, and allowed to respond for the self-infusion of 0, 0.03, 0.1, 0.3, 1.0 or 3.0 microM SAL into the posterior or anterior VTA. In a second experiment, rats self-administered 0.3 microM SAL for the initial 4 sessions, co-administered SAL with ICS-205,930 (a 5-HT3 receptor antagonist) or quinpirole (a D(2,3) receptor agonist) for sessions 5 and 6, and then only 0.3 microM SAL for session 7. RESULTS Wistar rats, given 0.03 to 0.3 microM SAL, received more infusions per session than did the group given artificial cerebrospinal fluid (aCSF) alone (e.g., 41 infusions for 0.1 microM SAL versus 9 infusions for the aCSF group), and responded more on the active than inactive lever. These effects were observed in the posterior but not in anterior VTA. Co-infusion of 100 microM ICS-205,930, or quinpirole significantly reduced self-infusions and active lever responding. CONCLUSIONS SAL produces reinforcing effects in the posterior VTA of Wistar rats, and these effects are mediated by activation of DA neurons and local 5-HT3 receptors.
An fMRI study of causal judgments

The capacity to evaluate causal relations is fundamental to human cognition, and yet little is known of its neurocognitive underpinnings. A functional magnetic resonance imaging study was performed to investigate an hypothesized dissociation between the use of semantic knowledge to evaluate specifically causal relations in contrast to general associative relations. Identical pairs of words were judged for causal or associative relations in different blocks of trials. Causal judgments, beyond associative judgments, generated distinct activation in left dorsolateral prefrontal cortex and right precuneus. These findings indicate that the evaluation of causal relations in semantic memory involves additional neural mechanisms relative to those required to evaluate associative relations.
On schemes of combinatorial transcription logic

Cells receive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate specific genetic responses. Here we explore theoretically the potentials and limitations of combinatorial signal integration at the level of cis-regulatory transcription control. Our analysis suggests that many complex transcription-control functions of the type encountered in higher eukaryotes are already implementable within the much simpler bacterial transcription system. Using a quantitative model of bacterial transcription and invoking only specific protein–DNA interaction and weak glue-like interaction between regulatory proteins, we show explicit schemes to implement regulatory logic functions of increasing complexity by appropriately selecting the strengths and arranging the relative positions of the relevant protein-binding DNA sequences in the cis-regulatory region. The architectures that emerge are naturally modular and evolvable. Our results suggest that the transcription regulatory apparatus is a “programmable” computing machine, belonging formally to the class of Boltzmann machines. Crucial to our results is the ability to regulate gene expression at a distance. In bacteria, this can be achieved for isolated genes via DNA looping controlled by the dimerization of DNA-bound proteins. However, if adopted extensively in the genome, long-distance interaction can cause unintentional intergenic cross talk, a detrimental side effect difficult to overcome by the known bacterial transcription-regulation systems. This may be a key factor limiting the genome-wide adoption of complex transcription control in bacteria. Implications of our findings for combinatorial transcription control in eukaryotes are discussed.
Distribution of Bemisia tabaci Genetic Groups in India

ABSTRACT The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a phloem-feeding, economically important pest of crops worldwide. In addition to direct damage, it also vectors a number of plant viruses belonging to the family Geminiviridae. Its populations differ biologically with respect to insecticide resistance, virus transmission and host range. Therefore, understanding genetic variation among populations is important for management. We sequenced 850 bp of the mitochondrial COI (mtCOI) gene from B. tabaci populations surveyed across India. BLAST analysis of the mtCOI sequences generated in this study with sequences from the mtCOI dataset showed the presence of one invasive group, MEAM1, and eight other groups of B. tabaci in India. mtCOI sequence analyses showed the presence of Asia I, Asia I-India, Asia II-1, Asia II-5, Asia II-7, Asia II-8, and Asia II-11 genetic groups. We also found China-3 in a field in Birbhum district, West Bengal, India, suggesting a role of anthropogenic activities in the distribution of B. tabaci. Interestingly, more than one genetic group was found coexisting in the same field.