Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental exploration on loss surface of deep neural network

The loss function of the deep neural network is high dimensional, nonconvex and complex. So far, the geometric properties of the loss surface of the neural network have not been well understood. Different from most theoretical studies on the loss surface, this article makes the experimental exploration on the loss surface of the deep neural network, including trajectories of various adaptive optimization algorithms, the Hessian matrix of the loss function of the deep neural network, the curvature of the loss surface along the trajectories of the various adaptive optimization algorithms. It is found that the gradient direction of the adaptive optimization algorithms is almost perpendicular to the direction of the maximum curvature of the loss surface, while the gradient directions of the stochastic gradient descent (SGD) algorithm do not have such a rule. The Hessian matrix of the loss surface along the trajectory of the optimization algorithm is degraded, which is inconsistent with the hypothetical that nonsingular of the Hessian matrix in many theoretical studies of deep learning. Besides, this article proposes a new ensemble learning method of the neural network based on the scaling invariance of the ReLu neural network and mode connectivity.
Does Dysdera crocata (Araneae Dysderidae) prefer woodlice as prey

Three different types of prey-preference tests were carried out using Dysdera crocata, a spider frequently described as a specialist predator of woodlice. None of these tests provided evidence that Dysdera crocata prefers woodlice over a variety of insect prey (house flies, beetle larvae, mirid bugs, moths and crickets). We also ran prey preference tests with two species of woodlice that differ in their behavioural and chemical defences, and there was no evidence of preference for either of these species over the other. The broader question of whether D. crocata is a specialized predator in any respect is discussed.
Genetic analysis of fish genomes and populations: allozyme variation within and among Atlantic salmon from Downeast rivers of Maine

Analysis of genetic variation within and among samples of naturally produced Atlantic salmon (n ¼ 372) from 7 Maine (U.S.A.) and one Canadian river were conducted based on 54 allozyme loci. Eight of the 54 loci proved polymorphic, and estimated heterozygosities (HS) based on all loci ranged from 0� 012 to 0� 026 (mean ¼ 0� 021, S.E. ¼ 0� 002). Only one of 56 tests revealed genotypic proportions that deviated significantly from Hardy–Weinberg expectations. Genetic distances (D) between samples ranged from 0� 002 to 0� 022. No obvious association existed between genetic and geographic distances. Cluster analysis of genetic distances revealed the Dennys River sample as the most differentiated when all samples were included in the analysis, though bootstrap support of the cluster analysis was generally weak. G-tests revealed significant differences in allele frequencies among samples at five of the polymorphic loci, and the G-value summed over all loci also indicated significant differences among samples. FST values indicated that 3� 4% of the total genetic diversity was due to variability among samples, while 96� 6% was due to variability within samples. These results indicate that the Atlantic salmon analyzed in this study had levels of genetic variability and differentiation among samples comparable to native populations from other areas collected across a similar geographic range.
The Use of a Motorway Wildlife Overpass By Large Mammals

We studied how mammals used a wildlife overpass across a motorway in central Netherlands using track counts in 1989, 1994 and 1995. Throughout the study the overpass was used most frequently by red deer (Cervus elaphus) and wild boar (Sus scrofa) and, less often, by roe deer (Capreolus capreolucs), red fox (Vulpes vulpes), fallow deer (Duma duma), Highland cattle, and badger (Meles meles). For red deer and wild boar the highest incidence of use was in autumn/early winter, correlating with the rutting season. Small mammals caught on the overpass were wood mouse (Apodemus sylvaticus), common vole (Microtus arvalis) and common shrew (Sorex araneus). The wildlife overpasses can be an effective means of connecting habitats for a wide range of mammals but the effectiveness is related to the width of the overpass. For large mammals a minimum width of 40-50 meters is recommended.
An update on DNA barcoding: low species coverage and numerous unidentified sequences

DNA barcoding was proposed in 2003, the Consortium for the Barcode of Life was established in 2004, and the movement has since attracted more than $80 million funding. Here we investigate how many species of multicellular animals have been barcoded. We compare the numbers in a public database (GenBank as of January 2012) with those in the Barcode of Life Database (BOLD) and find that GenBank contains COI (cytochrome c oxidase subunit 1) sequences for ca. 60 000 species while BOLD reports barcodes for ca. 150 000 species. The discrepancy is likely due to a large amount of unpublished data in BOLD. Overall, the species coverage remains sparse, growth rates are low, and the barcode accumulation curve for Metazoa is linear with only 4788 species having been added in 2011. In addition, the vast majority of species in the public database (73%) were barcoded by projects that are unlikely to be related to the DNA barcoding movement. Particularly surprising was the large number of DNA barcodes in GenBank that were not identified to species (Jan 2012: 74%), with insect barcodes often being identified only to order. Of these several hundred thousand have since been suppressed by NCBI because they did not satisfy the iBOL/GenBank early release agreement. Species coverage is considerably better for target taxa of DNA barcoding campaigns (e.g. birds, fishes, Lepidoptera), although it also falls short of published campaign targets.
Descriptions of two new Iridodrilus species and a re-examination of the earthworm genera Heliodrilus Beddard, Iridodrilus Beddard and Segunia Sims (Annelida: Oligochaeta: Eudrilidae)

This paper describes two new earthworm species, Iridodrilus codonothecoformis sp. n. and Iridodrilus condylopapillaris sp. n. and illustrates the major diagnostic features of, and the differences between, Iridodrilus roseus Beddard, 1897 and Heliodrilus lagosensis Beddard, 1890. Hitherto unnoticed features of I. roseus are also illustrated, namely that it possesses a bursa copulatrix and that two pairs of very tiny penial setae in sacs occasionally occur which penetrate the bursa copulatrix. It is also demonstrated that the structures hitherto regarded as a ‘coelomic duct’ that supposedly links the two fertilization chambers is in fact a pair of ovarian ducts that lead from the paired ovaries to the chambers; these ducts are not interlinked. It is further argued that neither Iridodrilus roseus nor Heliodrilus lagosensis can be regarded as having a spermathecal system that is paired internally. The implications of these findings are discussed in relation to the taxonomy of the two named genera. It is recom.
Analyse des variations individuelles en nutrition animale : application de l'analyse en composantes principales à l'étude de la secrétion lipidique du lait de chèvre

l,es résultats expérimentaux en nutrition des animaux domestiques sont souvent difficilement interprétables à cause des variations interindividuelles. Celles-ci sont en effet importantes; elles varient suivant le caractère étudié et sont, de ce fait, difficilement maîtrisables a priori dans un plan expérimental. Les résultats obtenus lors d’une expérimentation sur chèvres laitières montrent que leur étude par analyse multivariate peut permettre de souligner les grands types de relations entre les animaux. Ainsi des chèvres assez apparentées présentent, indépendamment des régimes et du stade physiologique, une matière grasse plus riche en acides gras courts et moyens associée à des teneurs plasmatiques en acétate, glucose et triglycérides plus importantes. Ce type d’approche permet d’exploiter la variance interindividuelle, donc de mieux connaître les exigences et les particularités nutritionnelles de chaque individu. En outre, elle permet d’envisager la maîtrise de ces variations en vue d’une interprétation plus fine ou d’une expérimentation ultérieure.
Students’ perception towards field study activity

This preliminary research aims to give description about students’ perception towards field study or about the reasons for students like or dislike field study activity which has been occurred at schools and the potency to conduct field trip learning. This research used quantitative survey research method with deep explanation. The data collection used questionnaire and interview. The statements in the questionnaire were open and close statements, which showed positive and negative perception with 5 point-Likert scales. Index of appreciation of field study were determined using questionnaire information from 19 students in 12th grade. The result show that out of 19 respondents, most of the express positive perception towards field study with average indices = 57.06 (range 45.45 – 81.82; with standard deviation = 8.48). The students’ positive perception towards field study activity implies can give impact toward field skills acquisition such as identification or classification skills, monitoring or sampling or survey skills, teamwork skill, and problem-solving skills in the field.
Spectrum of β‐thalassemia in Jordan: Identification of two novel mutations

Two hundred and forty‐four β‐thalassemia alleles were identified from 135 unrelated occasionally and periodically transfusion dependent β‐ and S/β‐thalassemia patients from all regions of Jordan. Allele identification was achieved by PCR amplification of β‐globin genes, dot‐blotting the amplified DNA, hybridization with allele specific synthetic probes, and direct sequencing of amplified genomic DNA. A total of 19 different mutations were detected, eight of them constituted about 86% of the Jordanian thalassemic chromosomes. These mutations were IVS1‐110 (G>A) (25%), IVS2‐1 (G>A) (15%), IVS2‐745 (C>G) (14.2%), IVS1‐1 (G>A) (10%), IVS1‐6 (T>C) (8.3%), codon 37 (G>A) (6.3%), codon 39 (C>T) (4.6%), and codon 5 (‐C) (3.8%). The remaining eleven mutations were rare, presented with frequencies ranging between 0.4% and 1.6%. These included two novel mutations and four others detected in Jordan for the first time. The novel mutations were the frame shift (‐C) at codon 49 and the substitution (A>C) at position −29 in the TATA box. Four alleles (1.6%) remained unidentified; having no abnormalities in their β‐globin gene sequences and therefore, constituted additional defects causing β‐thalassemia in the Jordanian population. These unknown alleles are expected to be candidates for upstream or downstream mutations affecting the expression of β‐globin gene. The results provided the essential foundation for planning a national preventive program for thalassemia in Jordan and will help improving the medical services for the patients and their families by helping their clinicians and genetic counselors in evaluating their variants and designing their treatment regimens. Am. J. Hematol. 68:16–22, 2001. © 2001 Wiley‐Liss, Inc.
The Economic Value of the Greater Yellowstone's Blue-Ribbon Fishery

Abstract The U.S. National Park Service must find a balance in an inherently conflicting mandate that calls for preserving and protecting ecological systems while providing for the public's enjoyment of natural resources through recreation. This conflict is especially intense in the case of fisheries management. Although most of the waters in Yellowstone National Park are managed as catch-and-release fisheries, some individuals still hold that fishing (like hunting) in the park is in fundamental conflict with the goal of preservation. An important element in the National Park Service's balancing act is the economic value of recreation activities. This paper uses the results of a 1993 survey of anglers at five blue-ribbon fishing sites in and near Yellowstone National Park to estimate the economic value that anglers attach to their fishing experiences. We estimate that fishermen place a value of between US$172 and $977 on a day of fishing. For Yellowstone National Park, these estimates translate into a tot.
Endophyte infection influences arbuscular mycorrhizal fungi communities in rhizosphere soils of host as opposed to non‐host grass

Endophytes live asymptomatically within many cool‐season grasses for at least a portion of their life cycle. Although the leaf endophyte effects on the growth and stress resistance of host grasses have been relatively well studied, less attention has been focused on how this relationship may impact soil microbial communities, especially arbuscular mycorrhizal fungi (AMF). We defined endophyte‐infected and endophyte‐free Leymus chinensis as the host grass and neighbouring Stipa krylovii, which was not infected by endophytes, as the non‐host grass. Our objective was to examine the effect of endophyte infection on the colonization rate and composition of AMF communities in both the rhizosphere and bulk soils of their host (L. chinensis) and a neighbouring non‐host (S. krylovii) by a consecutive 2‐year survey. We described AMF communities using high‐throughput DNA sequencing, quantified the proportion of root length colonized by AMF using microscopy, and estimated AMF biomass using a lipid biomarker. Structural equation modelling (SEM) was applied to disentangle the direct and indirect effects (mediated by multiple environmental factors) of an endophyte on AMF. We found that endophyte infection significantly increased colonization rates and rhizosphere soil biomass of AMF but had no significant effect on the bulk soil around the host grass. The endophyte increased the diversity of the rhizosphere soil AMF community by decreasing the abundance of the dominant species Glomus while increasing the abundance of some unidentified AMF. SEM showed that the endophyte effects on AMF biomass in rhizosphere soil were primarily mediated by soil total carbon, total nitrogen and pH. With respect to the non‐host grass, the endophyte infection of host grass did not change the colonization rates or AMF biomass in either the rhizosphere or bulk soil but did cause a shift in the rhizosphere soil AMF community composition, resulting in a decrease in the relative abundance of Septoglomus and an increase in the relative abundance of some unidentified AMF.
USING FIRST‐PASSAGE TIME IN THE ANALYSIS OF AREA‐RESTRICTED SEARCH AND HABITAT SELECTION

How animals change their movement patterns in relation to the environment is a central topic in a wide area of ecology, including foraging ecology, habitat selection, and spatial population ecology. To understand the underlying behavioral mechanisms in- volved, there is a need for methods to measure changes in movement patterns along a pathway through the landscape. We used simulated pathways and satellite tracking of a long-ranging seabird to explore the properties of first-passage time as a measure of search effort along a path. The first-passage time is defined as the time required for an animal to cross a circle with a given radius. It is a measure of how much time an animal uses within a given area. First-passage time is scale dependent, and a plot of variance in first-passage time vs. spatial scale reveals the spatial scale at which the animal concentrates its search effort. By averaging the first-passage time on a geographical grid, it is possible to relate first-passage time to environmental variables and the search pattern of other individuals.
Investigating young water fractions in a small Mediterranean mountain catchment: Both precipitation forcing and sampling frequency matter

The proportion of water younger than 2–3 months (young water fraction, Fyw) has become increasingly investigated in catchment hydrology. Fyw is typically estimated by comparing seasonal tracer cycles in precipitation and streamflow, through water sampling. However, some open research questions remain, such as: (i) whether part of the summer precipitation should be discarded because the high evapotranspiration demand, (ii) how well Fyw serves as a metric to compare catchments, and (iii) how sampling frequency affects Fyw estimates. To address these questions, we investigated Fyw in soil‐, ground‐ and stream waters for the small Mediterranean Can Vila catchment. Rainfall was sampled at 5‐mm intervals. Mobile soil water and groundwater were sampled fortnightly. Stream water was sampled depending on flow at variable time intervals (30 min to 1 week). Over 58 months, this sampling provided 1,529 δ18O determinations. Isotopic analyses results led us to include summer precipitation in the input signal. We found the highest Fyw in mobile soil waters (34%), while this was almost zero for groundwater except during wet periods. For stream waters, Fyw depended on the discharge variations, so that the flow‐weighted young water fraction ( Fyw* ) was 22.6%, whereas the time‐weighted Fyw was just 6.2%. Both Fyw* and its discharge sensitivity (Sd) varied when different 12‐month sampling periods were investigated. The young water fraction that would be obtained from a virtual thorough sampling ( Fyw** ) was estimated from the Sd and the observed stream flow. This showed an underestimation of Fyw** by 25% for the frequent dynamic sampling and 66% for weekly sampling, due to missing high flows. Our results confirm that Fyw and its discharge sensitivity are metrics very sensitive to meteorological forcing during the analysed period. Thus, comparisons between catchments need long‐term mean annual values and their variability. Our findings also support the dependence of Fyw estimates on the sampling rate and show the advantages of flow‐weighted analysis. Finally, catchment water turnover investigations should be accompanied by the analysis of flow duration curves.
Effects of Hunting on Response Behaviors of Wild Reindeer

Abstract Because wild reindeer (Rangifer tarandus) are hunted in southern Norway, reindeer may perceive all recreationists as threats. Potential adverse effects of hunting on reindeer behavior may be exacerbated by other forms of recreation because the number of skiers and hikers in areas inhabited by reindeer has also increased. The Norefjell–Reinsjøfjell wild reindeer area is used extensively for recreation and tourism. Reindeer hunting was introduced in the area in 1992, and harvest rate has been stable at about 38% of winter herd size. We recorded behavioral responses of reindeer to a person approaching directly on foot or skis during 1992 and again in 2002–2006. Compared to 1992, flight-initiation distance increased and fewer groups assessed the observer before taking flight during 2002–2006. In winter, when reindeer are usually comparably more vigilant than in other seasons, flight-initiation distance increased from only 60 m to 115 m and escape distance decreased from 400 m to 210 m. Neither alert distance, calf carcass weights (23.6 ± 0.7 [SE] kg to 22.4 ± 0.2 kg), nor reindeer herd size (661 ± 73 to 579 ± 15) changed during the 15 years of our study. Reindeer appeared to habituate to the observer because they initiated flight at shorter distances as the number of approaches on the same day increased. In Norefjell–Reinsjøfjell, encounters with a person on foot or skis did not result in behavioral responses likely to entail substantial energy costs for reindeer; therefore, hunting at current levels appears compatible with other recreational activities.
Effects of hydrologically confined fishes on bacterioplankton and autotrophic picoplankton in a semiarid marsh

An enclosure experiment was conducted to assess the separate effects of exotic benthivorous (Cyprinus carpio L.), planktivorous (Gambusia holbrooki Gir.), and omnivorous (Lepomis gibbosus L.) fish on the dynamics of bacterioplankton (BAC) and autotrophic picoplankton (APP) in a semiarid Spanish marsh. Special emphasis was put on simulating the effect of natural fish density situations occur- ring under periods of hydrological confinement in the wet- land, i.e. during summer draw downs or artificial water-level reductions, when fish biomass can reach high levels. The resulting simulation of such a scenario (C. carpio, 5000 to 6000 kg ha -1 ; L. gibbosus, 1300 to 1700 kg ha -1 , and G. hol- brooki, 115 kg ha -1 ) revealed that C. carpio and L. gibbosus significantly increased the trophic level in the enclosures. This resulted in a significant increase of BAC in the respective treatments. G. holbrooki, on the other hand, failed to fuel BAC growth. Considering APP, composed of phycocyanin- rich picocyanobacteria Synechococcus sp. , no fish treatment effects were detected, suggesting that the fishes, indepen- dent of biomasses used, were not important in driving APP. Results indicate that microbial communities respond in differ- ent ways to changes in fish biomass in fluctuating wetlands.
Water Resources Management Strategies for Irrigated Agriculture in the Indus Basin of Pakistan

Agriculture of Pakistan relies on the Indus basin, which is facing severe water scarcity conditions. Poor irrigation practices and lack of policy reforms are major threats for water and food security of the country. In this research, alternative water-saving strategies are evaluated through a high spatio-temporal water footprint (WF) assessment (1997–2016) for the Punjab and Sindh provinces, which cover an irrigated area of 17 million hectares in the Indus basin of Pakistan. The SPARE:WATER model is used as a spatial decision support tool to calculate the WF and establish alternative management plans for more sustainable water use. The average water consumption (WFarea) is estimated to 182 km3 yr−1, composed of 75% blue water (irrigation water from surface water and groundwater sources), 17% green water (precipitation) and 8% grey water (water used to remove soil salinity or dilute saline irrigation water). Sugarcane, cotton, and rice are highly water-intensive crops, which consume 57% of the annual water use. However, WFarea can be reduced by up to 35% through optimized cropping patterns of the existing crops with the current irrigation settings and even by up to 50% through the combined implementation of optimal cropping patterns and improved irrigation technologies, i.e., sprinkler and drip irrigation. We recommend that the economic impact of these water-saving strategies should be investigated in future studies to inform stakeholders and policymakers to achieve a more sustainable water policy for Pakistan.
Time‐Series Analysis of Volume Change at Brady Hot Springs, Nevada, USA, Using Geodetic Data From 2003–2018

Brady Hot Springs geothermal field has exhibited subsidence, as measured by interferometric synthetic aperture radar (InSAR). Previous studies have examined both the temporal evolution of the deformation from 2004 through 2016 and the spatial extent of the deformation, directly relating the observed subsidence to volumetric changes below the surface. We extend the modeling at Brady to analyze a data set of interferometric pairs spanning from the end of 2003 through 2018. We examine spatial and temporal trends in the observed deformation by time‐series analysis of each of the 1,656 cubic voxels in a parameterized elastic dislocation model to identify areas where the subsurface volume changes as a function of time. Joint time‐series analysis of Global Positioning System and InSAR pairs confirm significant changes in rates of volume change during time intervals when well operations were varied. The rate of subsidence increases with increased injection, consistent with the identification of thermal contraction of the rock matrix as the dominant driving mechanism. Conversely, the modeled volume increases when pumping ceases, suggesting thermal expansion of the rock matrix.