Miracle-dz/UniFAR-FTUs huggingface dataset:
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models

Background Sequence alignment lies at the heart of genome sequence annotation. While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). The Forward algorithm that provides much of pHMMs’ sensitivity is relatively slow, motivating extensive efforts to increase speed. Numerous researchers have devised methods to improve pHMM alignment speed using hardware accelerators such as graphics processing units (GPUs) and field programmable gate arrays (FPGAs). Here, we describe an FPGA hardware accelerator for a key bottleneck step in the analysis pipeline employed by the popular pHMM aligment tool, HMMER. HMMER accelerates pHMM Forward alignment by screening most sequence with a series of filters that rapidly approximate the result of computing full Forward alignment. The first of these filters, the Single Segment ungapped Viterbi (SSV) algorithm, is designed to filter out 98% of non-related inputs and accounts for 70% of the overall runtime of the DNA search tool nhmmer in common use cases. SSV is an ideal target for hardware acceleration due to its limited data dependency structure. Results We present Hardware Accelerated single segment Viterbi Additional Coprocessor (HAVAC), an FPGA-based hardware accelerator for the SSV algorithm. The core HAVAC kernel calculates the SSV matrix at 1739 GCUPS on a Xilinx Alveo U50 FPGA accelerator card, ∼ 227x faster than the optimized SSV implementation in nhmmer. Accounting for PCI-e data transfer data processing, HAVAC is 65x faster than nhmmer’s SSV with one thread and 35x faster than nhmmer with four threads, and uses ∼ 31% the energy of a traditional high end Intel CPU. Because these computations are performed on a co-processor, the host CPU remain free to simultaneously compute downstream pHMM alignment and later post-processing. Author summary Sequence alignment lies at the heart of genome sequence annotation, and must be both fast and accurate. Signals of relationships between sequences are obscured over time by mutational forces, so that alignment and annotation of the full diversity of life demands highly sensitive tools. Profile hidden Markov models (pHMMs) provide the greatest sensitivity in the face of diversity, but are relatively slow. Here, we describe an approach to improving the speed of pHMM search that leverages field programmable gate arrays - hardware devices that can be configured to implement arbitrary digital circuits to achieve impressive parallelism and energy efficiency. Our tool, HAVAC, accelerates one key bottleneck step in the analysis pipeline employed by the popular pHMM aligment tool, HMMER. HAVAC produces a ∼ 60x speedup over the analogous stage in HMMER. HAVAC can be implemented as a part of a larger sequence homology search tool for faster search times and reduced energy usage. Interested users can download HAVAC on github at https://github.com/TravisWheelerLab/HAVAC.
Radiographic changes of the pelvis in Labrador and Golden Retrievers after juvenile pubic symphysiodesis

Summary Objectives: The hypothesis of this study was that juvenile pubic symphysiodesis (JPS) results in pelvic changes that can be identified radiographically in adult dogs. Methods: The medical records at the Clinica Veterinaria Vezzoni were searched for standard ventro-dorsal views of the pelvis of adult Labrador and Golden Retrievers that had undergone JPS or had not undergone surgery. The objective assessment of radiographs included the analysis of various pelvic measurements. Subjective evaluation of radiographs was undertaken by 18 specialists and 21 general practitioners and was based on five criteria relating to 1) the acetabular fossae, 2) the pubic symphysis, 3) the margin of the cranial pubic area, 4) the pubic rami, and 5) the obturator foramen. Results: The radiographs of 42 Labrador Retrievers and 16 Golden Retrievers were evaluated. The most useful criteria were the radiographic measurement of the shape of the obturator foramen and two different ratios of length to width of the pubic rami; these values were significantly smaller in dogs after JPS. The pelvic canal width was the same in both groups. All objective measurements were repeatable within and between evaluators. The most reliable subjective criterion was number 4, followed by number 5 in Golden Retrievers and by 2 in Labrador Retrievers. Conclusion: Our objective and subjective evaluations were simple and yielded useful and repeatable results. There was no significant difference between general practitioners and specialists with regard to subjective evaluation, which indicates that these evaluation criteria can be used by small animal clinicians after minimal training.
METEOROLOGY AND CLIMATE: PROBLEMS AND EXPECTATIONS

The predictive power of differential non linear equations weakly coupled, in the description of elementary processes by far more rigorously known than those existing in Meteorology and Climatology where the differential equations are strongly coupled, is discussed in order to call attention on the claimed predictive power in the field of Meteorology and Climate change where problems must necessarily be by far more complex. Years of work and strong financial support are needed in order to improve the theoretical formulation of these problems and the corresponding experimental worldwide observations. This is necessary before anyone can claim that a scientific rigorous understanding has been achieved in mastering all Meteorology and Climate change problems of the past, present and future.
Variations in magma supply rate at Kilauea Volcano, Hawaii

When an eruption of Kilauea lasts more than 4 months, so that a well-defined conduit has time to develop, magma moves freely through the volcano from a deep source to the eruptive site at a constant rate of 0.09 km3/yr. At other times, the magma supply rate to Kilauea, estimated from geodetic measurements of surface displacements, may be different. For example, after a large withdrawal of magma from the summit reservoir, such as during a rift zone eruption, the magma supply rate is high initially but then lessens and exponentially decays as the reservoir refills. Different episodes of refilling may have different average rates of magma supply. During four year-long episodes in the 1960s, the annual rate of refilling varied from 0.02 to 0.18 km3/yr, bracketing the sustained eruptive rate of 0.09 km3/yr. For decade-long or longer periods, our estimate of magma supply rate is based on long-term changes in eruptive rate. We use eruptive rate because after a few dozen eruptions the volume of magma that passes through the summit reservoir is much larger than the net change of volume of magma stored within Kilauea. The low eruptive rate of 0.009 km3/yr between 1840 and 1950, compared to an average eruptive rate of 0.05 km3/yr since 1950, suggests that the magma supply rate was lower between 1840 and 1950 than it has been since 1950. An obvious difference in activity before and since 1950 was the frequency of rift zone eruptions: eight rift zone eruptions occurred between 1840 and 1950, but more than 20 rift zone eruptions have occurred since 1950. The frequency of rift zone eruptions influences magma supply rate by suddenly lowering pressure of the summit magma reservoir, which feeds magma to rift zone eruptions. A temporary drop of reservoir pressure means a larger-than-normal pressure difference between the reservoir and a deeper source, so magma is forced to move upward into Kilauea at a faster rate.
Direct measurement of the mantle attenuation operator from broadband P and S Waveforms

Displacement and velocity records of P and SH body waves with broadband frequency content from 0.01 to 5.0 Hz are obtained either directly or through multichannel deconvolution of earthquake waveforms from digitally recording stations of the Global Digital Seismographic Network, the Regional Seismic Test Network, and the Graefenberg array. Source parameters of a deep focus earthquake are determined by modeling P waveforms with a dynamically realistic source model and a model of Qα that is allowed to be frequency-dependent. Because the phase behavior predicted by intrinsic attenuation often contrasts sharply with that predicted by realistic rupture models, there are strong constraints on source and attenuation operators. Using the rupture model derived from the P waves and neglecting the effects of scattering, a search is made for the minimum phase operators required to obtain matches to the observed S waves. The variation in the inferred minimum phase operator between S and ScS phases and its behavior with increasing distance and frequency are used to estimate a depth- and frequency-dependent model of intrinsic Qβ. Strong constraints on the frequency dependence of Qβ are given by fine details in the shape and dispersion of the broadband displacements of the S waves. Rise times are most sensitive to the higher end of the frequency band (0.2–1.0 Hz), while the pulse width and tail are sensitive to the lower end of the frequency band (0.01–0.2 Hz). Although the frequency dependence of the derived tβ* is quite simple, having smooth decreases from 0.01 to 5.0 Hz, a relatively complex parameterization of the frequency and depth dependence of Q is required to match this frequency dependence. Either the power n in a frequency-dependent Q = Cfn varies with depth, the high-frequency cutoff in the relaxation spectrum varies with depth, or both. The midmantle between depths of 400 and 1600 km contributes primarily to the attenuation of low frequencies (0.01–0.1 Hz) of body waves. Below the mantle depth of 2000 km the P and S waveforms for the paths investigated suggest that little or no attenuation exists in the band of 0.01–5 Hz.
Drought Assessments Using Satellite-based Drought Index in Korea; Southern Region Case in 2013

가뭄은 자연재난 중 다른 재난에 비해서 영향면적이 넓으며, 시간적으로도 장기간에 걸쳐 느린 속도로 영향을 미치게 된 다. 홍수, 산사태, 강풍 피해 등 단기간에 집중적으로 영향을 미치는 경우와 달리 가뭄의 전조를 감지하고 진행되는 영향 범위를 파악하는 것은 매우 어려운 과정이라 할 수 있다. 이 상고온현상의 지속, 강우의 부족 등의 이상 기후 현상은 최근 들어 광범위하게 발생하고 있으며, 기후변화로 인해 전망되는 다양한 예측치들은 가뭄 재해에 악영향을 미칠 것으로 파악 된다(IPCC, 2007). 국립기상연구소의 기후변화 시나리오 보 고서(2011)에 따르면 우리나라를 포함한 동아시아 지역은 기 후변화로 인한 강수량 증가가 예상된다. 이러한 강우의 평균 적인 증가는 기후변화에서 흔히 예측되는 시나리오이지만, 이 Abstract
Lichenometric dating of debris‐flow deposits on alpine colluvial fans in Southwest Norway

Lichenometry provides a suitable means of dating recent debris-flow activity on alpine colluvial fans. Existing growth curves can be used, provided that anomalous thalli are excluded and allowances are made for differences in the growth rates of Rhizocarpon alpieola and Rhizocarpon section Rhizocarpon thalli. The distribution of flow deposits through time is non-random and two periods of increased activity (1670-1720 AD and 1790-1860 AD) can be identified. There is no evidence for a large increase in debris-flow activity in the late 19th century, as has been found in Scotland. This can be attributed to the absence of detrimental landuse practices in the Norwegian study areas.
Extension of stochastic volatility equity models with the Hull–White interest rate process

We present an extension of stochastic volatility equity models by a stochastic Hull–White interest rate component while assuming non-zero correlations between the underlying processes. We place these systems of stochastic differential equations in the class of affine jump-diffusion–linear quadratic jump-diffusion processes so that the pricing of European products can be efficiently performed within the Fourier cosine expansion pricing framework. We compare the new stochastic volatility Schöbel–Zhu–Hull–White hybrid model with a Heston–Hull–White model, and also apply the models to price hybrid structured derivatives that combine the equity and interest rate asset classes.
Alongshore variation in beach cusp morphology in a coastal embayment

The variation in beach cusp characteristics was examined along a 1km long embayed beach (Pearl Beach, New South Wales, Australia). The beach cusp morphology had formed during the previous day and/or night and displayed a marked alongshore variation in cusp spacing. The edge wave mechanism of beach cusp formation could not account for the observed trend in cusp spacing, because no relationship could be established between the spacing of the cusps and the gradient of the beachface. On the other hand, the cusp spacing was strongly related to the horizontal swash excursion, providing some support for the self-organization model of beach cusp formation. Copyright# 1999 John Wiley & Sons, Ltd.
The tectonic setting of the Fiordland region, south-west New Zealand

Summary. The Indian/Pacific plate boundary to the south-west of New Zealand has undergone highly oblique compression during the past 15 Myr. Subduction of the Indian plate north-eastwards under the Pacific plate has probably occurred at Puysegur Trench, south of New Zealand, for most of this period. In contrast, subduction at the plate boundary through south-west New Zealand (Fiordland) has only occurred during the last 7Myr when oceanic lithosphere of the Indian plate has been adjacent to the continental lithosphere of Fiordland (Pacific plate). Transcurrent motion at the plate boundary during this time has transferred the continental lithosphere forming Challenger Plateau on the Indian plate northwards relative to southern New Zealand. Most geophysical features of the Fiordland region can be accounted for in terms of this recent subduction event at the Fiordland margin. However, the intermediate depth seismicity appears to arise from a fragment of the Indian plate, subducted at Puysegur Trench and subsequently moved northwards by the transcurrent motion between the two plates.
Effects of urbanization and industrialization on the hydrological regime and on water quality

About 180 engineers and scientists from 27 countries attended the International Symposium on the Effects of Urbanization and Industrialization on the Hydrological Regime and on Water Quality. The symposium was held at Amsterdam, the Netherlands, October 2–7, 1977. The symposium was convened by the United Nations Educational, Scientific, and Cultural Organization (Unesco) and organized by Unesco and the Netherlands National Committee for the International Hydrological Programme in cooperation with the International Association of Hydrological Sciences. The 64 technical papers for the symposium covered three themes. The first theme dealt with the effects of urbanization and industrialization on the hydrological regime, the second concentrated on the effect of urbanization and industrialization on water quality, and the third centered on water policy as a factor in urbanization and industrialization. Each theme was broken into sessions comprising 4–8 papers. Each session was followed by a discussion period in which the speakers responded to questions raised by the audience. These questions and answers were recorded and presented to the technical secretary. The symposium focused within the framework of project 7 of the International Hydrological Programme and is related to the Workshop on Socioeconomic Aspects of Urban Hydrology held at Lund, Sweden, in November 1976. Following the symposium, the Workshop on the Impact of Urbanization and Industrialization on Regional and National Water Planning and Management was convened at the Netherlands, October 10–13, 1977. Participation in the workshop was by invitation only.
Live Well, Eat Well, Be Active With Diabetes Curriculum Improves Type 2 Diabetes Management

Type 2 diabetes is a complex disease with several modifiable lifestyle factors. The Extension ‘Live well, Eat well, be Active with Diabetes’ curriculum provides four 90-minute lessons teaching individuals to live well, eat well, and be active with diabetes. Fourteen Extension educators implemented and evaluated the curriculum with 107 participants. Participants reported the program helped them feel better able to take care of their health. We observed significant differences in participants’ retrospective pre and post ‘Live well,’ ‘Eat well’ and ‘be Active’ total scores. Extension has a unique opportunity to educate individuals so they may better manage their diabetes.
Influence of ENSO and the Atlantic Multidecadal Oscillation on Drought over the United States

Abstract Composites based on observations and model outputs from the Climate Variability and Predictability (CLIVAR) drought experiments were used to examine the impact of El Nino–Southern Oscillation (ENSO) and the Atlantic multidecadal oscillation (AMO) on drought over the United States. Because drought implies persistent dryness, the 6-month standardized precipitation index, standardized runoff index, and soil moisture anomalies are used to represent drought. The experiments were performed by forcing an AGCM with prescribed sea surface temperature anomalies (SSTAs) superimposed on the monthly mean SST climatology. Four model outputs from the NCEP Global Forecast System (GFS), NASA’s Seasonal-to-Interannual Prediction Project, version 1 (NSIPP1), GFDL’s global atmospheric model, version 2.1 (AM2.1), and the Lamont-Doherty Earth Observatory (LDEO)/NCAR Community Climate System Model, version 3 (CCM3) were analyzed in this study. Each run lasts from 36 to 51 yr. The impact of ENSO on drought over the Unit.
El espacio urbano nocturno de la ciudad de Murcia

We study the night urban space structure at Murcia, from the hypothesis according to which this structure strongly depends on the distribution of party and music pubs and its social perception. By a registry of pubs, Lynch model and surveys, we have defined four principle functional areas at night, which are substructured by a particular way. As factors that more define social perception, we highlight the age of space users and its interests when going out at night. The work ends with a schematic graphic representation of real night urban space.
Influence of Added Aluminum on Carbon Dioxide Production in Tropical Soils

Aluminum added to a yellow-brown Latosol, as Al₂(SO₄)₃, at rates of 6.6, 16.5, and 33.0 meg /100 g of soil decreased soil pH from 5.9 to 4.6, 4.0 and 3.8, respectively. Carbon dioxide production during 35 days of incubation decreased with increases in H-ion concentration. In an attempt to separate the effects of H-ion displacement from that of Al-ion hydrolysis on microbial activity, Al-treated soils were left unadjusted, or adjusted to pH 4.0, 5.5 or 6.5 before incubation. Carbon dioxide production decreased with increases in added Al when the soil pH was maintained below about 4.0. Aluminum precipitated rather rapidly in soils with a higher pH and the Al had little influence on CO₂ production. Less than 1 ppm of Al was extracted by 1n KCl when the final pH of the soil was above approximately 4.0 (as determined in neutral salt). Below this range, exchangeable Al increased with increases in amounts of Al initially added to the soil. In a second experiment, a highly significant negative linear relationship was found between CO₂ production and increasing percentages of Al in mixtures of Al- and Ca-saturated Everglades muck. Furthermore, when Ca-saturated muck was adjusted to pH 4.0 with HCl, and incubated, the production of CO₂ was significantly greater than in Al-saturated muck adjusted to pH 4.0. Since exchangeable Al did not increase when the Ca-saturated muck was adjusted to a lower pH, but did increase when the pH of the Al-saturated muck was lowered, it appeared that Al had an influence on CO₂ production in these acid soils.
East Antarctic sea ice: Albedo, thickness distribution, and snow cover

Characteristics of springtime sea ice off East Antarctica were investigated during a cruise of the Australian National Antarctic Research Expedition in October through December 1988. The fractional coverage of the ocean surface, the ice thickness, and the snow cover thickness for each of several ice types were estimated hourly for the region near the ship. These observations were carried out continuously during the 4 weeks the ship was in the ice. Thin and young ice types were prevalent throughout the region, and the observations show a systematic increase in the total area-weighted pack ice thickness (including open water area) from only 0.2 m within 50 km of the ice edge to 0.45 m close to the coast. Ice thickness averaged over the ice-covered region only is also relatively thin, ranging from 0.35 m near the ice edge to 0.65 m in the interior. These values are probably typical of average winter thickness for the area. The average snow cover thickness on the ice increased from 0.05 m near the ice edge to 0.15 m in the interior. Average ice concentration increased from less than 6/10 near the ice edge to 8/10 in the interior. The ship-observed concentrations were in good agreement with concentrations derived from passive microwave satellite imagery except in some regions of high concentration. In these regions the satellite-derived concentrations were consistently lower than those estimated from the ship, possibly because of the inability of the satellite sensors to discriminate the appreciable percentage of very thin ice observed within the total area. Spectral albedo was measured for nilas, young grey ice, grey-white ice, snow-covered ice, and open water at wavelengths from 420 to 1000 nm. Allwave albedo was computed by using the spectral measurements together with estimates of near-infrared albedo and modeled spectral solar flux. Area-averaged albedos for the East Antarctic sea ice zone in spring were derived from representative allwave albedos together with the hourly observations of ice types. These area-averaged surface albedos increased from about 0.35 at the ice edge to about 0.5 at 350 km from the edge, remaining at 0.5 to the coast of Antarctica. The low average albedo is in part due to the large fraction of open water within the pack, but extensive fractions of almost snow-free thin ice also play an important role.
Fossil Fuels Running out: Third Generation Micro Algal Biofuels Showing Light of Hope

Fossil fuels have become the most important part of our lives and they play a very important role in our daily life. Because of increasing population and very high demands of fossil fuels, there will be shortage of these energy resources and there is a fear of depletion of these natural resources. The life is very much dependent of petrol, diesel and other fossil fuels which are being used in our daily activities and the shortage of fossil fuels is making them expensive at each and every minute, so there is a need for economical fuel. The biofuel are the solution for world’s fuel problems. The biofuel are the renewable and the carbon free source of fuel which is good for environment also. The first generations by fuels produced from plants were questionable due to their conflicts with food crops and productivity of oil. The microalgae is capable of producing 10 - 100 times higher oil content than the crops producing oil. The growing and harvesting of microalgae is easier and extraction of oil from biomass is also an economical process and hence seems to be very promising future of biofuel or economical fuels.
Fishery and Reef Management

Callum M. Roberts (Reports, 21 Nov., p. [1454][1]) uses a model of reef connectivity to identify beneficial management partnerships and to evaluate marine reserves in integrated networks. The model is clear and compelling. But, like others based on similar approaches ([1][2]), it makes one