Miracle-dz/UniFAR-FTUs huggingface dataset:
Iceberg Scour and Shell Damage in the Antarctic Bivalve Laternula elliptica

We document differences in shell damage and shell thickness in a bivalve mollusc (Laternula elliptica) from seven sites around Antarctica with differing exposures to ice movement. These range from 60% of the sea bed impacted by ice per year (Hangar Cove, Antarctic Peninsula) to those protected by virtually permanent sea ice cover (McMurdo Sound). Patterns of shell damage consistent with blunt force trauma were observed in populations where ice scour frequently occurs; damage repair frequencies and the thickness of shells correlated positively with the frequency of iceberg scour at the different sites with the highest repair rates and thicker shells at Hangar Cove (74.2% of animals damaged) compared to the other less impacted sites (less than 10% at McMurdo Sound). Genetic analysis of population structure using Amplified Fragment Length Polymorphisms (AFLPs) revealed no genetic differences between the two sites showing the greatest difference in shell morphology and repair rates. Taken together, our results suggest that L. elliptica exhibits considerable phenotypic plasticity in response to geographic variation in physical disturbance.
Polymer photodetector with voltage-adjustable photocurrent spectrum

Polymer photodetectors with voltage-adjustable photoresponse from visible to near infrared range are demonstrated. Poly(3-hexylthiophene) and (6,6)-phenyl-C61-butyric acid methyl ester (PCBM) blend is used as the active layer. The photoresponse can be continuously adjusted by the thickness of the active layer as well as the applied voltage bias. The thickness of the active layer is varied from 250 nm to 16.2 μm. The mechanism for the photoresponse adjusted by the thickness can be attributed to the absorption of the photons in the infrared range by thick PCBM layer. The mechanism for the photoresponse adjusted by the applied bias can be attributed to the carrier recombination reduction when the applied bias increases. The adjustable photodetector also has high operating speed up to 10 kHz.
Models of Behavior Deviations in Model-Based Systems

Tasks like diagnosis, failure-modes-and-effects analysis (FMEA), and therapy proposal involve reasoning about variables and parameters deviating from some reference state. In model-based systems, one tries to capture this kind of inferences by models that describe how such deviations are emerging and propagated through a system. Several techniques and systems have been developed that address this issue, in particular in the area of qualitative modeling. However, to our knowledge, a rigorous mathematical foundation and a "recipe" for how to construct such compositional deviation models has not been presented in the literature, despite the widespread use of the idea and the techniques. In this paper, we present a general mathematical formalization of deviation models. Based on this, aspects of constructing libraries of deviation models, their properties, and their application in consistency-based diagnosis and prediction-based FMEA in a component-oriented framework are analyzed.
Automatic optic disc and optic cup detection in retinal images acquired by mobile phone

Medical image processing plays an important role in the automatic detection of certain eye diseases, disease documentation, treatment monitoring and educational purposes. The continuous improvement of the hardware of mobile phones gives us the ability to capture images like this. Interesting question can be: are these images suitable for automatic image processing, or more specifically, how much information can be obtained from this kind of images? In this paper, we would like to investigate whether a mobile device suitable to use as a medical diagnostic tool. We present a comparison between images made by a mobile device and a clinical eye examination one. We perform optic disc and optic cup detection from which we calculate cup to disc ratio. Our results show that images acquired by mobile phone are suitable for automatic image processing. Beyond these, a database of images were set up to allow researchers to test their algorithms and methods for image processing.
Coding of Visual Object Features and Feature Conjunctions in the Human Brain

Object recognition is achieved through neural mechanisms reliant on the activity of distributed coordinated neural assemblies. In the initial steps of this process, an object's features are thought to be coded very rapidly in distinct neural assemblies. These features play different functional roles in the recognition process - while colour facilitates recognition, additional contours and edges delay it. Here, we selectively varied the amount and role of object features in an entry-level categorization paradigm and related them to the electrical activity of the human brain. We found that early synchronizations (approx. 100 ms) increased quantitatively when more image features had to be coded, without reflecting their qualitative contribution to the recognition process. Later activity (approx. 200–400 ms) was modulated by the representational role of object features. These findings demonstrate that although early synchronizations may be sufficient for relatively crude discrimination of objects in visual scenes, they cannot support entry-level categorization. This was subserved by later processes of object model selection, which utilized the representational value of object features such as colour or edges to select the appropriate model and achieve identification.
Minimum-weight triangulation is NP-hard

A triangulation of a planar point set S is a maximal plane straight-line graph with vertex set S. In the minimum-weight triangulation (MWT) problem, we are looking for a triangulation of a given point set that minimizes the sum of the edge lengths. We prove that the decision version of this problem is NP-hard, using a reduction from PLANAR 1-IN-3-SAT. The correct working of the gadgets is established with computer assistance, using dynamic programming on polygonal faces, as well as the β-skeleton heuristic to certify that certain edges belong to the minimum-weight triangulation.
Relating Equity and Credit Markets through Structural Models: Evidence from Volatilities

This paper examines the connection between the return volatilities of credit market securities, equities, and Treasuries using a Merton model with stochastic interest rates. Focusing primarily on monthly bond and CDS returns, we find that the credit market exhibits volatility in excess of what the equity market and the Merton model suggest. In conjunction with the evidence in Schaefer and Strebulaev (2008), this suggests that while the co-movement of returns in the credit and equity markets can be characterized correctly on average by a Merton model, the value in credit markets sometimes deviates from fundamentals. Furthermore, we find that the excess volatility in credit markets is associated with less liquid issues and issues with poorer ratings, but does not appear to be worse at the height of the Financial Crisis.
Context Gates for Neural Machine Translation

In neural machine translation (NMT), generation of a target word depends on both source and target contexts. We find that source contexts have a direct impact on the adequacy of a translation while target contexts affect the fluency. Intuitively, generation of a content word should rely more on the source context and generation of a functional word should rely more on the target context. Due to the lack of effective control over the influence from source and target contexts, conventional NMT tends to yield fluent but inadequate translations. To address this problem, we propose context gates which dynamically control the ratios at which source and target contexts contribute to the generation of target words. In this way, we can enhance both the adequacy and fluency of NMT with more careful control of the information flow from contexts. Experiments show that our approach significantly improves upon a standard attention-based NMT system by +2.3 BLEU points.
Plasmodium falciparum Isolates in India Exhibit a Progressive Increase in Mutations Associated with Sulfadoxine-Pyrimethamine Resistance

ABSTRACT The combination of sulfadoxine-pyrimethamine (SP) is used as a second line of therapy for the treatment of uncomplicated chloroquine-resistant Plasmodium falciparum malaria. Resistance to SP arises due to certain point mutations in the genes for the dihydrofolate reductase (DHFR) and dihydropteroate synthetase (DHPS) enzymes of the parasite. We have analyzed these mutations in 312 field isolates of P. falciparum collected from different parts of India to assess the effects of drug pressure. The rate of mutation in the gene for DHFR was found to be higher than that in the gene for DHPS, although the latter had mutations in more alleles. There was a temporal rise in the number of isolates with double dhfr mutations and single dhps mutations, resulting in an increased total number of mutations in the loci for DHFR and DHPS combined over a 5-year period. During these 5 years, the number of isolates with drug-sensitive genotypes decreased and the number of isolates with drug-resistant genotypes (double DHFR mutations and a single DHPS mutation) increased significantly. The number of isolates with the triple mutations in each of the genes for the two enzymes (for a total of six mutations), however, remained very low, coinciding with the very low rate of SP treatment failure in the country. There was a regional bias in the mutation rate, as isolates from the northeastern region (the state of Assam) showed higher rates of mutation and more complex genotypes than isolates from the other regions. It was concluded that even though SP is prescribed as a second line of treatment in India, the mutations associated with SP resistance continue to be progressively increasing.
Congenital hydrocephalus and ventriculoperitoneal shunts: influence of etiology and programmable shunts on revisions.

OBJECT Hydrocephalus is a notorious neurosurgical disease that carries the adage "once a shunt always a shunt. " This study was conducted to review the treatment results of pediatric hydrocephalus. METHODS Pediatric patients who underwent ventriculoperitoneal shunt surgery over the past 14 years were reviewed for shunt revisions. Variables studied included age at shunt placement, revision, or replacement; programmable shunts; infection; obstruction; and diagnosis (congenital, posthemorrhagic, craniospinal dysraphism, and others including trauma, tumors, and infection). Multiple regression analysis methods were used to determine independent risk factors for shunt failure and the number of shunt revisions. The Kaplan-Meier method of survival analysis was used to compare etiologies on the 5-year survival (revision-free) rate and the median 5-year survival time. RESULTS A total of 253 patients were studied with an almost equal sex distribution. There were 92 patients with congenital hydrocephalus, 69 with posthemorrhagic hydrocephalus, 48 with craniospinal dysraphism, and 44 with other causes. Programmable shunts were used in 73 patients (other types of shunts were used in 180 patients). A total of 197 patients (78%) underwent revision surgeries due to shunt failures. The mortality rate was 1.6%. Age at first revision, the 5-year survival rate, and the median 5-year survival time were significantly less for both posthemorrhagic and craniospinal dysraphism than for either the congenital or "other" group (p < 0.05). The failure rate and number of revisions were not significantly reduced with programmable shunts compared with either pressure-controlled or no-valve shunts (p > 0.5). CONCLUSIONS Posthemorrhagic hydrocephalus and craniospinal dysraphism hydrocephalus had significantly earlier revisions than congenital and other etiologies. Programmable systems did not reduce the failure rate or the average number of shunts revisions.
K+ Channel Expression and Cell Proliferation Are Regulated by Intracellular Sodium and Membrane Depolarization in Oligodendrocyte Progenitor Cells

The effects of a variety of antiproliferative agents on voltage-dependent K+ channel function in cortical oligodendrocyte progenitor (O-2A) cells were studied. Previously, we had shown that glutamate receptor activation reversibly inhibited O-2A cell proliferation stimulated by mitogenic factors and prevented lineage progression by attenuating outward K+ currents in O-2A cells. We now show that the antiproliferative actions of glutamate receptor activation are Ca2+-independent and arise from an increase in intracellular Na+ and subsequent block of outward K+ currents. In support of this mechanism, agents that acted to depolarize O-2A cells or increase intracellular sodium similarly had an antiproliferative effect, attributable at least in part to a reduction in voltage-gated K+ currents. Also, these effects were reversible and Ca2+-independent. Chronic treatment with glutamate agonists was without any long-term effect on K+ current function. Cells cultured in elevated K+, however, demonstrated an upregulation of inward rectifier K+ currents, concomitant with an hyperpolarization of the resting membrane potential. This culture condition therefore promoted a current phenotype typical of pro-oligodendroblasts. Finally, cells chronically treated with the mitotic inhibitor retinoic acid displayed a selective downregulation of outward K+ currents. In conclusion, signals that affect O-2A cell proliferation do so by regulating K+ channel function. These data indicate that the regulation of K+currents in cells of the oligodendrocyte lineage plays an important role in determining their proliferative potential and demonstrate that O-2A cell K+ current phenotype can be modified by long-term depolarization of the cell membrane.
Comment on “Expression of Helios, an Ikaros Transcription Factor Family Member, Differentiates Thymic-Derived from Peripherally Induced Foxp3+ T Regulatory Cells”

We haven taken into consideration A.S. Bhagwat's comment concerning the mechanism of β-elimination by the endonuclease VIII (Nei) enzyme. Our conclusion that deoxyuridine triphosphate incorporation happens during somatic hypermutation of murine VkOx genes relies on the following results: the
Genomic analyses of African Trypanozoon strains to assess evolutionary relationships and identify markers for strain identification

African trypanosomes of the sub-genus Trypanozoon) are eukaryotic parasitesthat cause disease in either humans or livestock. The development of genomic resources can be of great use to those interested in studying and controlling the spread of these trypanosomes. Here we present a large comparative analysis of Trypanozoon whole genomes, 83 in total, including human and animal infective African trypanosomes: 21 T. brucei brucei, 22 T. b. gambiense, 35 T. b. rhodesiense and 4 T. evansi strains, of which 21 were from Uganda. We constructed a maximum likelihood phylogeny based on 162,210 single nucleotide polymorphisms (SNPs.) The three Trypanosoma brucei sub-species and Trypanosoma evansi are not monophyletic, confirming earlier studies that indicated high similarity among Trypanosoma “sub-species”. We also used discriminant analysis of principal components (DAPC) on the same set of SNPs, identifying seven genetic clusters. These clusters do not correspond well with existing taxonomic classifications, in agreement with the phylogenetic analysis. Geographic origin is reflected in both the phylogeny and clustering analysis. Finally, we used sparse linear discriminant analysis to rank SNPs by their informativeness in differentiating the strains in our data set. As few as 84 SNPs can completely distinguish the strains used in our study, and discriminant analysis was still able to detect genetic structure using as few as 10 SNPs. Our results reinforce earlier results of high genetic similarity between the African Trypanozoon. Despite this, a small subset of SNPs can be used to identify genetic markers that can be used for strain identification or other epidemiological investigations.
Cardiovascular safety of stimulants in children with attention-deficit/hyperactivity disorder: a nationwide prospective cohort study.

OBJECTIVE The purpose of this study was to determine whether stimulant users are at higher risk of a later cardiovascular event than are non-users, examining this association in both a national cohort and a population-based sample of children and adolescents diagnosed with attention-deficit/hyperactivity disorder (ADHD). We also aim to examine a possible dose-response relationship in such an association. METHODS We conducted a longitudinal, prospective cohort study of all children born in Denmark between 1990 and 1999. Within this cohort, children with ADHD were identified. Data from national health registers on psychiatric and somatic diagnoses, stimulant prescriptions, cardiovascular risk factors, pre- and perinatal and sociodemographic covariates in all children and their parents were merged, using the unique personal identification number. Hazard ratios (HR) for cardiovascular events were estimated using Cox regression, adjusted for other known risk factors. RESULTS In the total population (n=714,258 contributing a total of 6,767,982 person-years) use of stimulants increased the risk of a cardiovascular event; adjusted HR=1.83 (1.10-3.04). In children with ADHD (n=8300) stimulant treatment also increased the risk of a cardiovascular event (adjusted HR=2.20 [2.15-2.24]), with a complex time-dependent dose-response relationship. CONCLUSIONS This is the first nationwide cohort study of the cardiovascular safety of stimulants in children and adolescents, and it represents, to our knowledge, the longest prospective follow-up study. Cardiovascular events were rare but twice as likely in stimulant users as in non-users, both in the total national population and in children with ADHD. We found a complex, time- and dose-dependent interrelationship between cardiovascular adverse events and stimulant treatment in children and adolescents. Our results suggest a safety signal with an increased risk of cardiovascular disease associated with stimulant treatment in children and adolescents, even after adjusting for a number of potential confounders.
Injection-Locked Magnetron Using a Cross-Domain Analyzer

An injection-locked magnetron with an external oscillator was investigated to obtain the parameters of the equivalent circuit model. The magnetron was locked over the ratio of the input power to output power of -26 dB and had the resonance characteristics of a parallel LCR circuit model. Increasing the input power caused the anti-resonance frequency to become the original frequency of the magnetron; the range of the locking frequency was wider because of the lower Q value. The phase noise of the locked magnetron of -70 dBc at a 40-kHz offset was improved in comparison with an unlocked magnetron. The results show that an injection-locked magnetron with an external oscillator has great potential for obtaining a high power output.
Farm level analysis of investment behaviours in soil conservation and erosion control practices in the ecologically vulnerable communities in Southeast Nigeria

This study analyzed the determinants of farm-level soil conservation investment behaviours in Southeast Nigeria. A probit econometric model was used to analyze data obtained from 480 randomly selected farm households from 12 erosion-prone communities in the region. The results show that younger farmers aged between 18-44 years cultivating at least 0.7 ha of land over which they have control in terms of allocation and usage had higher probabilities of investing in the conservation practices compared to the older farmers. Investment decisions increased with increased farm households’ own liquidity, off-farm income, knowledge of the practices through extension contacts, level of formal education, ownership and control over cultivated lands, length of land lease, membership in farmers’ associations, and farm sizes greater than the mean farm size of 0.7ha. But insecurity of land tenure generally increased farmers’ risk of appropriation of input resources and decreased investments in the practices, especially for the female farmers who do not have title to land in the area. Investments in the practices also decreased with increased family sizes and the erosion-induced land scarcity conditions in the region. The study confirms the importance of recognizing the heterogeneity of the farming population not only in terms of the biophysical conditions of their farms but also the socioeconomic and demographic conditions under which they operate. Extension efforts in Southeast Nigeria should therefore target the younger farmers and promote projects aimed at developing offfarm enterprises, since these positively influence household liquidity and investments in conservation practices.
The eukaryotic initiation factor eIF4H facilitates loop-binding, repetitive RNA unwinding by the eIF4A DEAD-box helicase

Eukaryotic translation initiation is a highly regulated process in protein synthesis. The principal translation initiation factor eIF4AI displays helicase activity, unwinding secondary structures in the mRNAs 5′-UTR. Single molecule fluorescence resonance energy transfer (sm-FRET) is applied here to directly observe and quantify the helicase activity of eIF4AI in the presence of the ancillary RNA-binding factor eIF4H. Results show that eIF4H can significantly enhance the helicase activity of eIF4AI by strongly binding both to loop structures within the RNA transcript as well as to eIF4AI. In the presence of ATP, the eIF4AI/eIF4H complex exhibits persistent rapid and repetitive cycles of unwinding and re-annealing. ATP titration assays suggest that this process consumes a single ATP molecule per cycle. In contrast, helicase unwinding activity does not occur in the presence of the non-hydrolysable analog ATP-γS. Based on our sm-FRET results, we propose an unwinding mechanism where eIF4AI/eIF4H can bind directly to loop structures to destabilize duplexes. Since eIF4AI is the prototypical example of a DEA(D/H)-box RNA helicase, it is highly likely that this unwinding mechanism is applicable to a myriad of DEAD-box helicases employed in RNA metabolism.
Detecting and resolving packet filter conflicts

Packet filters are rules for classifying packets based on their header fields. Packet classification is essential to routers supporting services such as quality of service (QoS), virtual private networks (VPNs), and firewalls. A filter conflict occurs when two or more filters overlap, creating an ambiguity in packet classification. Current techniques for resolving filter conflicts are based on prioritizing conflicting filters, and choosing the higher priority filter. We show that such ordering does not always work. Instead, we propose a new scheme for conflict resolution, which is based on the idea of adding resolve filters. Our main results are algorithms for detecting and resolving conflicts in a filter database. We have tried our algorithm on 3 existing firewall databases, and have found conflicts, which are potential security holes, in each of them.