Miracle-dz/UniFAR-FTUs huggingface dataset:
Congestion-driven regional re-clustering for low-cost FPGAs

FPGA device area is dominated by a limited amount of interconnect. CAD tools must meet a hard channel-width constraint for a circuit to be successfully mapped to a device. Previous work has shown that if a design cannot be mapped to a device due to insufficient interconnect availability, it is possible to identify regions of high interconnect demand and spread out the logic in this area into surrounding regions. This is done by re-packing logic in the affected regions into an increased number of CLBs. This increases the effective amount of interconnect in these high-demand areas. This methodology has been shown to significantly reduce channel width, at the expense of CLB count and runtime. In this paper, we extend this previous algorithm in two ways: we present novel region selection techniques to optimize the selection of which regions should be depopulated, and we introduce a local channel-width demand model which can be used to more accurately determine the amount of white space insertion at each iteration. Together, these techniques lead to significant run-time improvements and reduce the area of the resulting FPGA implementations. We were able to improve runtime by a factor of up to 5.5 times while reducing area by up to 20% when compared to previous methods.
Radiographic evaluation of early periprosthetic femoral bone contrast and prosthetic stem alignment after uncemented and cemented total hip replacement in dogs.

OBJECTIVE To radiographically evaluate periprosthetic femoral bone contrast and assess alignment of the prosthetic stem after uncemented and cemented total hip replacement (THR). STUDY DESIGN Prospective clinical study. ANIMALS Dogs (n = 15). METHODS Dogs were classified into uncemented (n = 8) and cemented (n = 7) THR groups. Radiographs were analyzed using image processing software to evaluate femoral bone contrast (gray scale value, GV) for each and combined modified Gruen zone(s) immediately and 4 months after THR. Modified Gruen zones were classified into 5 zones to analyze retrospectively the regional radiographic GV of the femur around uncemented and cemented prosthetic stem. Alignment of prosthetic stem was assessed immediately and 4 months postoperatively. Variables were compared by use of 2-tailed t-test, with P < . 05 considered significant. RESULTS Zone 1 showed significant decrease in the mean bone GV 4 months after uncemented THR. No differences in zones 1-5 after 4 months of cemented THR. Combined zones showed significant decrease in overall mean bone GV 4 months after uncemented THR. No changes were observed 4 months after cemented THR. Number of limbs with varus-aligned femoral stem markedly increased after 4 months of uncemented THR. CONCLUSIONS Regional bone contrast and prosthetic stem alignment vary with the design of THR.
In vitro activity of the polyether ionophorous antibiotic monensin against the cyst form of Toxoplasma gondii

We have studied the activity of the polyether ionophorous antibiotic monensin against the cyst form (bradyzoite) of Toxoplasma gondii. The experiments were conducted in vitro using 2 methods; cysts produced either in mice or in cell culture were exposed to monensin in vitro, and the infectivity of the parasites was then assessed in vivo or in vitro. The data obtained from these 2 systems of evaluation showed that monensin inhibits the infectivity and the viability of the bradyzoites. Its activity was time and concentration dependent. The first effects were observed at very low drug concentrations (i.e. 0·0001 μg/ml). Immunofluorescence and electron microscopy analysis showed significant cytological alterations of the monensin-treated bradyzoites: they were swollen, had a large number of vacuoles in their cytoplasm and were found lysed at higher concentrations in ionophore.
Alteration of CAIs as recorded by 36S/34S as a function of 35Cl/34S

Using new model calculations, we study the production of chlorine and sulfur isotopes in different irradiation scenarios. We demonstrate that irradiation during meteorite transit from the asteroid belt to Earth has a negligible influence on the sulfur isotopic composition. We analyzed five different physical assemblages: carbonaceous chondrites, carbonaceous chondrites covered with water ice, carbonaceous chondrites covered with water ice that contains silicates and chlorine, precursor CAIs, and water ice that contains chlorine. For each of these five we ran simulations in which they were irradiated by galactic cosmic rays or solar energetic particles. We found that for producing sufficient amounts of 36Cl, the required GCR and SEP flux densities must have been either unreasonably high on absolute terms or must had been high relatively late after the formation of the solar system. This finding casts doubt on the interpretation of the correlation lines in the diagram 36S/34S and 35Cl/34S as isochrons. Alternatively, the correlation may be interpreted as mixing between water that contains chlorine that has been irradiated (likely as ice) either by GCR or SEP particles and sulfur (without any chlorine) with solar isotopic composition. Using this model we can explain the correlation as mixing between components, one of which was exposed to energetic particles; the conditions of this irradiation are not unrealistic.
Dopamine drives Drosophila sechellia adaptation to its toxic host

Many insect species are host-obligate specialists. The evolutionary mechanism driving the adaptation of a species to a toxic host is, however, intriguing. We analyzed the tight association of Drosophila sechellia to its sole host, the fruit of Morinda citrifolia, which is toxic to other members of the melanogaster species group. Molecular polymorphisms in the dopamine regulatory protein Catsup cause infertility in D. sechellia due to maternal arrest of oogenesis. In its natural host, the fruit compensates for the impaired maternal dopamine metabolism with the precursor l-DOPA, resuming oogenesis and stimulating egg production. l-DOPA present in morinda additionally increases the size of D. sechellia eggs, what in turn enhances early fitness. We argue that the need of l-DOPA for successful reproduction has driven D. sechellia to become an M. citrifolia obligate specialist. This study illustrates how an insect's dopaminergic system can sustain ecological adaptations by modulating ontogenesis and development. DOI: http://dx.doi. org/10.7554/eLife.03785. 001
Systemic Chemotherapy and White Matter Integrity in Tracts Associated with Cognition Among Children With Neurofibromatosis Type 1

Children with neurofibromatosis type 1 (NF1) are predisposed to both brain tumors and cognitive deficits. While changes in white matter integrity after multimodal therapy are associated with cognitive dysfunction, the effect of isolated chemotherapy in NF1 is unknown. To determine whether chemotherapy is associated with white matter microstructural changes, we examined diffusion tensor imaging (DTI) in NF1 subjects.
Predicting all-cause risk of 30-day hospital readmission using artificial neural networks

Avoidable hospital readmissions not only contribute to the high costs of healthcare in the US, but also have an impact on the quality of care for patients. Large scale adoption of Electronic Health Records (EHR) has created the opportunity to proactively identify patients with high risk of hospital readmission, and apply effective interventions to mitigate that risk. To that end, in the past, numerous machine-learning models have been employed to predict the risk of 30-day hospital readmission. However, the need for an accurate and real-time predictive model, suitable for hospital setting applications still exists. Here, using data from more than 300,000 hospital stays in California from Sutter Health’s EHR system, we built and tested an artificial neural network (NN) model based on Google’s TensorFlow library. Through comparison with other traditional and non-traditional models, we demonstrated that neural networks are great candidates to capture the complexity and interdependency of various data fields in EHRs. LACE, the current industry standard, showed a precision (PPV) of 0.20 in identifying high-risk patients in our database. In contrast, our NN model yielded a PPV of 0.24, which is a 20% improvement over LACE. Additionally, we discussed the predictive power of Social Determinants of Health (SDoH) data, and presented a simple cost analysis to assist hospitalists in implementing helpful and cost-effective post-discharge interventions.
DNA Methylation and Gene Expression Profiling of Ewing Sarcoma Primary Tumors Reveal Genes That Are Potential Targets of Epigenetic Inactivation

The role of aberrant DNA methylation in Ewing sarcoma is not completely understood. The methylation status of 503 genes in 52 formalin-fixed paraffin-embedded EWS tumors and 3 EWS cell lines was compared to human mesenchymal stem cell primary cultures (hMSCs) using bead chip methylation analysis. Relative expression of methylated genes was assessed in 5-Aza-2-deoxycytidine-(5-AZA)-treated EWS cell lines and in a cohort of primary EWS samples and hMSCs by gene expression and quantitative RT-PCR. 129 genes demonstrated statistically significant hypermethylation in EWS tumors compared to hMSCs. Thirty-six genes were profoundly methylated in EWS and unmethylated in hMSCs. 5-AZA treatment of EWS cell lines resulted in upregulation of expression of hundreds of genes including 162 that were increased by at least 2-fold. The expression of 19 of 36 candidate hypermethylated genes was increased following 5-AZA. Analysis of gene expression from an independent cohort of tumors confirmed decreased expression of six of nineteen hypermethylated genes (AXL, COL1A1, CYP1B1, LYN, SERPINE1,) and VCAN. Comparing gene expression and DNA methylation analyses proved to be an effective way to identify genes epigenetically regulated in EWS. Further investigation is ongoing to elucidate the role of these epigenetic alterations in EWS pathogenesis.
Histogenesis of mouse cerebellum in microwell cultures. Cell reaggregation and migration, fiber and synapse formation

A microwell culture system was developed for analysis of cell movements and interactions during nervous system histogenesis. Cells from trypsinized 7-day-old mouse cerebellum reaggregated within hours into clusters which later developed interconnections consisting of either sheets of migrating cells and cell processes or cables of fiber bundles with cells migrating along their surfaces. Granule cells in several stages of differentiation, basket and/or stellate neurons, some larger neurons, and two types of neuroglial cells were identified in reproducible, nonrandom patterns by scanning and transmission electron microscopy. Axonal and dendritic processes, both with growth cones, and numerous synapses were generated in vitro.
Epidemic spreading on complex networks with general degree and weight distributions

The spread of disease on complex networks has attracted wide attention in the physics community. Recent works have demonstrated that heterogeneous degree and weight distributions have a significant influence on the epidemic dynamics. In this study, a novel edge-weight-based compartmental approach is developed to estimate the epidemic threshold and epidemic size (final infected density) on networks with general degree and weight distributions, and a remarkable agreement with numerics is obtained. Even in complex networks with the strong heterogeneous degree and weight distributions, this approach is used. We then propose an edge-weight-based removal strategy with different biases and find that such a strategy can effectively control the spread of epidemic when the highly weighted edges are preferentially removed, especially when the weight distribution of a network is extremely heterogenous. The theoretical results from the suggested method can accurately predict the above removal effectiveness.
Avoiding traceroute anomalies with Paris traceroute

Traceroute is widely used, from the diagnosis of network problems to the assemblage of internet maps. However, there are a few serious problems with this tool, in particular due to the presence of load balancing routers in the network. This paper describes a number of anomalies that arise in nearly all traceroute-based measurements. We categorize them as "loops", "cycles", and "diamonds". We provide a new publicly-available traceroute, called Paris traceroute, which controls packet header contents to obtain a more precise picture of the actual routes that packets follow. This new tool allows us to find conclusive explanations for some of the anomalies, and to suggest possible causes for others.
Spatial and temporal deposition of selected biogeochemical important trace species in South Africa

_____________________________________________________________________________________ The concern of potential adverse environmental effects due to increased anthropogenic emissions to the atmosphere necessitates the need for long-term atmospheric deposition programmes. Wet and dry depositions of emitted chemical species to the earth’s surface play an essential role in controlling the concentration of gases and aerosols in the troposphere. The chemical content of atmospheric deposition is the signature of several interacting physical and chemical mechanisms such as emission and source amplitude; transport in and dynamics of the atmosphere; atmospheric chemical reactions; and removal processes. The importance of atmospheric deposition as a source of nutrients and key trace elements, i.e. nitrogen (N), sulphur (S), carbon (C) and base metals, is widely recognised (Duce et al., 2009), while it could also be a source of toxic species (Greaver et al., 2012). It is therefore important to establish atmospheric budgets of key chemical compounds to understand the functioning of ecosystems and biogeochemical cycles (Dentener et al., 2006; Davidson et al., 2012). The study of deposition therefore allows for the tracing of the temporal and spatial evolution of atmospheric chemistry and is a pertinent indicator to evaluate natural and anthropogenic influences. Atmospheric chemistry determines the natural and anthropogenic makeup and abundance of pollutant species such as aerosols and gases on a regional scale (Isaksen et al., 2009). It is important to monitor the rates of deposition in order to assess the impact of deposited pollutants on terrestrial and aquatic ecosystems. This study focused on the total dry gaseous deposition and wet deposition of selected biogeochemically important trace species in South Africa. This study also contributed greatly to the database available for scientists in this field, since limited data on this subject is available for South Africa. This study includes measurement data for gaseous species as well as rainwater species in an attempt to assist future global deposition estimations. The sites for the current study are Amersfoort (AF), Louis Trichardt (LT) and Vaal Triangle (VT) (located on the South African Highveld), and Skukuza (SK), which is situated in the South African Lowveld. These sites are considered to be regionally representative of the north-eastern interior of South Africa. Two of these sites are in the region where the major anthropogenic emission sources in South Africa are situated.
Interaction among Agents that Block End‐plate Depolarization Competitively

The influence of gallamine, metocurine, pancuronium, and tubocurarine on depolarization of a mammalian muscle end-plate region was examined to determine whether the antagonists given in combination exerted a degree of block consistent with the simple classical competitive model. Depolarization was produced by carbachol in isolated guinea pig lumbrical muscles and recorded by the moving fluid electrode technique. The dose–response values obtained were fitted to a regression embedded in a split plot factorial experimental design such as both to control and to measure effects of variation among preparations, order of administration, time, and level of block. Of the six possible pairings of the four drugs, four showed the simple additivity expected from a competitive mechanism, while two (pancuronium plus metocurine and metocurine plus gallamine) showed potentiation beyond additivity. In these latter two pairs the combination shifted the carbachol dose-response curve, respectively, 41 and 21% further than predicted from the classical model. The significance of this deviation in the light of alternative receptor models is discussed, and a model consistent with the observed results is outlined.
Bitstream-Based JPEG Encryption in Real-time

The authors propose a framework to encrypt Baseline JPEG files directly at bitstream level, i.e., without the need to recompress them. The authors' approach enables encrypting more than 25 pictures per second in VGA resolution, allowing real-time operation in typical video surveillance applications. In addition, their approach preserves the length of the bitstream while being completely format-compliant. Furthermore, the authors show that an attack on the encryption process, which partly relies on AES, is practically infeasible.
Matrix Completion With Column Manipulation: Near-Optimal Sample-Robustness-Rank Tradeoffs

This paper considers the problem of matrix completion when some number of the columns are completely and arbitrarily corrupted, potentially by a malicious adversary. It is well known that standard algorithms for matrix completion can return arbitrarily poor results, if even a single column is corrupted. One direct application comes from robust collaborative filtering. Here, some number of users are so-called manipulators who try to skew the predictions of the algorithm by calibrating their inputs to the system. In this paper, we develop an efficient algorithm for this problem based on a combination of a trimming procedure and a convex program that minimizes the nuclear norm and the ℓ1,2 norm. Our theoretical results show that given a vanishing fraction of observed entries, it is nevertheless possible to complete the underlying matrix even when the number of corrupted columns grows. Significantly, our results hold without any assumptions on the locations or values of the observed entries of the manipulated columns. Moreover, we show by an information-theoretic argument that our guarantees are nearly optimal in terms of the fraction of sampled entries on the authentic columns, the fraction of corrupted columns, and the rank of the underlying matrix. Our results therefore sharply characterize the tradeoffs between sample, robustness, and rank in matrix completion.
Prenatal Polybrominated Diphenyl Ether Exposures and Neurodevelopment in U.S. Children through 5 Years of Age: The HOME Study

Background: Polybrominated diphenyl ethers (PBDEs) are persistent chemicals that have been widely used as flame retardants in furniture, carpet padding, car seats, and other consumer products during the past three decades. Objective: We examined whether in utero exposure to PBDEs is associated with child cognitive function and behavior in a U.S. study sample. Methods: In a prospective birth cohort, we measured maternal serum concentrations of BDE-47 and other PBDE congeners in 309 women at 16 weeks of gestation during 2003–2006 and followed their children in Cincinnati, Ohio. We measured cognitive and motor abilities using the Bayley Scales of Infant Development-II at ages 1, 2, and 3 years; intelligence using the Wechsler Preschool and Primary Scale of Intelligence-III at age 5 years; and children’s behaviors using the Behavioral Assessment System for Children-2 annually at ages 2–5 years. We used linear mixed models or generalized estimating equations with adjustment for potential confounders to estimate associations between these outcomes and log10-transformed PBDE concentrations. Results: The geometric mean of BDE-47 in maternal serum (20.1 ng/g lipid) was comparable with U.S. adult national reference values. Prenatal BDE-47 was not significantly associated with Bayley Mental or Psychomotor Development Indices at 1–3 years, but a 10-fold increase in prenatal BDE-47 was associated with a 4.5-point decrease (95% CI: –8.8, –0.1) in Full-Scale IQ and a 3.3-point increase (95% CI: 0.3, 6.3) in the hyperactivity score at age 5 years. Conclusions: Prenatal exposure to PBDEs was associated with lower IQ and higher hyperactivity scores in children. Citation: Chen A, Yolton K, Rauch SA, Webster GM, Hornung R, Sjödin A, Dietrich KN, Lanphear BP. 2014. Prenatal polybrominated diphenyl ether exposures and neurodevelopment in U.S. children through 5 years of age: the HOME study. Environ Health Perspect 122:856–862; http://dx.doi. org/10.1289/ehp.1307562
Signal Transduction in Astrocytes during Chronic or Acute Treatment with Drugs (SSRIs, Antibipolar Drugs, GABA-ergic Drugs, and Benzodiazepines) Ameliorating Mood Disorders

Chronic treatment with fluoxetine or other so-called serotonin-specific reuptake inhibitor antidepressants (SSRIs) or with a lithium salt “lithium”, carbamazepine, or valproic acid, the three classical antibipolar drugs, exerts a multitude of effects on astrocytes, which in turn modulate astrocyte-neuronal interactions and brain function. In the case of the SSRIs, they are to a large extent due to 5-HT2B-mediated upregulation and editing of genes. These alterations induce alteration in effects of cPLA2, GluK2, and the 5-HT2B receptor, probably including increases in both glucose metabolism and glycogen turnover, which in combination have therapeutic effect on major depression. The ability of increased levels of extracellular K+ to increase [Ca2+]i is increased as a sign of increased K+-induced excitability in astrocytes. Acute anxiolytic drug treatment with benzodiazepines or GABAA receptor stimulation has similar glycogenolysis-enhancing effects. The antibipolar drugs induce intracellular alkalinization in astrocytes with lithium acting on one acid extruder and carbamazepine and valproic acid on a different acid extruder. They inhibit K+-induced and transmitter-induced increase of astrocytic [Ca2+]i and thereby probably excitability. In several cases, they exert different changes in gene expression than SSRIs, determined both in cultured astrocytes and in freshly isolated astrocytes from drug-treated animals.
Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India

Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States–sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population.