Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipschitz Certificates for Neural Network Structures Driven by Averaged Activation Operators

Obtaining sharp Lipschitz constants for feed-forward neural networks is essential to assess their robust-ness in the face of perturbations of their inputs. We derive such constants in the context of a general layered network model involving compositions of nonexpansive averaged operators and affine operators. By exploiting this architecture, our analysis finely captures the interactions between the layers, yielding tighter Lipschitz constants than those resulting from the product of individual bounds for groups of layers. The proposed framework is shown to cover in particular most practical instances encountered in feed-forward neural networks. Our Lipschitz constant estimates are further improved in the case of structures employing scalar nonlinear functions, which include standard convolutional networks as special cases.
Microbacterium flavum sp. nov. and Microbacterium lacus sp. nov., isolated from marine environments.

Strains YM18-098T and A5E-52T were both Gram-positive, aerobic, irregular rod-shaped bacteria, with lysine and ornithine as the diagnostic diamino acids of their peptidoglycans, respectively. The acyl type of the peptidoglycan in both cases was N-glycolyl. The major menaquinones were MK-11, -12 and -13. Mycolic acids were not detected. The G+C content of the DNA was 69–70 mol%. Comparative 16S rRNA studies revealed that the isolates belonged to the genus Microbacterium, that YM18-098T was closely related to the species Microbacterium lacticum and Microbacterium schleiferi, and that A5E-52T was closely related to the species Microbacterium aurum, Microbacterium aoyamense, Microbacterium deminutum and Microbacterium pumilum. DNA-DNA relatedness analysis showed that the isolated strains represented two separate genomic species. Based on both phenotypic and genotypic data, the following new species of the genus Microbacterium are proposed: Microbacterium flavum sp. nov. and Microbacterium lacus sp. nov., with the type strains YM18-098T (= MBIC08278T, DSM 18909T) and A5E-52T (= MBIC08279T, DSM 18910T), respectively.
In vitro models for processes involved in intestinal absorption

The abundance of different techniques and protocols available reflects the need for reliable in vitro methods to assess intestinal absorption of potentially bioactive compounds. Physicochemical assays try to pinpoint the molecular properties contributing to the absorption process. The end points of biologically based methods, such as cell cultures and excised tissues, account for all processes undergone by a molecule that traverses a ‘living’ biological membrane, a cell or tissue. On top of fundamental physical processes (e.g., solubility, diffusion) such biological methods incorporate physiological responses such as active transport and metabolism. In this review, an account of in vitro methods for the assessment of molecular properties (lipophilicity, solubility, permeability) influencing intestinal absorption is given. Their advantages and limitations and the possibilities offered by this area of research are also evaluated. The combination of results from both classes of assays (physicochemical and biological) and integration with computational models will guide future developments in this field. Finally, possible future developments including stem cell research and multiple-end point assays are discussed.
STUDIES ON BEEF EATING QUALITY IN RELATION TO THE CURRENT CANADA GRADE CLASSIFICATIONS

The eating quality, cooking losses and chemical composition of semitendinosus (ST) and longissimus dorsi (LD) roasts from 48 young steers weighing 475–513 kg and representing Canada Grade A1 to A4, B1 and an unofficial grade of A1X (dairy-type) beef carcasses were determined. There was a tendency for Grade A4 and A1X ST and LD samples to be higher in percent fat (ether extract) than comparable samples from the other grades. In spite of fat differences in the muscles among grades, subjective evaluation of the eating quality of the roasts by a trained panel indicated that ST and LD roasts from all of the grades were acceptable and quite similar. However, judges did note the presence of larger amounts of fat in those beef samples which contained greater amounts of chemically determined fat (A4, A1X). Consumer panel judgements of ST roasts were similar to those of the trained judges. Objective measurements of juiciness (water-holding capacity) and tenderness (Warner Bratzler shear. Kramer shear) for ST and LD.
Potential impact of climate change on selected agricultural crops in north‐eastern Austria

The vulnerability and adaptation of major agricultural crops to various soils in north‐eastern Austria under a changing climate were investigated. The CERES crop model for winter wheat and the CROPGRO model for soybean were validated for the agrometeorological conditions in the selected region. The simulated winter wheat and soybean yields in most cases agreed with the measured data. Several incremental and transient global circulation model (GCM) climate change scenarios were created and used in the study. In these scenarios, annual temperatures in the selected region are expected to rise between 0.9 and 4.8 °C from the 2020s to the 2080s. The results show that warming will decrease the crop‐growing duration of the selected crops. For winter wheat, a gradual increase in air temperature resulted in a yield decrease. Incremental warming, especially in combination with an increase in precipitation, leads to higher soybean yield. A drier climate will reduce soybean yield, especially on soils with low water storage capacity. All transient GCM climate change scenarios for the 21st century, including the adjustment for only air temperature, precipitation and solar radiation, projected reductions of winter wheat yield. However, when the direct effect of increased levels of CO2 concentration was assumed, all GCM climate change scenarios projected an increase in winter wheat yield in the region. The increase in simulated soybean yield for the 21st century was primarily because of the positive impact of warming and especially of the beneficial influence of the direct CO2 effect. Changes in climate variability were found to affect winter wheat and soybean yield in various ways. Results from the adaptation assessments suggest that changes in sowing date, winter wheat and soybean cultivar selection could significantly affect crop production in the 21st century.
Predicting site-specific overwintering of juvenile brown trout (Salmo trutta) using a habitat suitability index

Brown trout (Salmo trutta) site-specific overwintering was studied in an ice-covered stream in northern Sweden. We monitored 238 individually tagged juvenile trout (body length 120–204 mm) from late summer until late winter using portable passive integrated transponder tag equipment and related it to a habitat suitability index. Minimum habitat suitability index explained a large portion (66.8%) of the variation in the proportion of individuals that remained and overwintered at specific sites from late summer until late winter. Our study design detected three scales of overwinter movements: (i) individuals that remained within their tagging site (site-scale movements); (ii) individuals that moved to other reaches (reach-scale movements), which were probably the most common; and (iii) individuals that left the study stream (stream-scale movements). There were no differences in size at tagging among individuals that adopted different scales of movements. We suggest that habitat suitability index can be used.
Plant isolation reduces outcross pollen receipt in a partially self‐compatible herb

1 Few studies of pollination success in fragmented systems measure stigmatic pollen load, and those that do often find it unrelated to plant or population density, size or isolation. Reduced reproductive output, however, is commonly reported, probably because incompatible pollen is contributing substantially to pollen loads of isolated flowers. 2 We used manipulated floral arrays of a bee‐pollinated species (Dianella revoluta) to investigate isolation effects on deposition of outcross pollen, while precluding self‐pollen transfer. 3 Outcross pollen receipt declined significantly over short distances up to approximately 50 m but even the most isolated flowers received some pollen grains. In contrast, heterospecific pollen did not decline, indicating that the outcross‐pollen decline was not due to reduced pollinator visitation. Increased distance of experimental arrays from a nature reserve did not reduce the probability of pollen receipt. 4 Many flowers were damaged by flower feeding beetles in the genus Arsipoda, which would be likely to substantially reduce the efficiency with which flowers are converted to fruits. The probability of flower damage from these predators was significantly lower in arrays that were more distant from the nature reserve. 5 This study indicates that reduced plant density and increased isolation from a source of outcrossed pollen can lead to a substantial decline in the probability of outcrossing, even when pollinator visitation is maintained at a high level. Depending on the mating system, this process will lead to reduced seed set or increased inbreeding for plants in fragmented habitats, even when pollinator abundance and behaviour are unaffected.
Correction: Aberrant DNA Methylation of Matrix Remodeling and Cell Adhesion Related Genes in Pterygium

Wanwen Lan was not included in the byline. This author should be listed as the third author and affiliated with Ocular Wound Healing and Therapeutics Laboratory, Singapore Eye Research Institute, Singapore, Singapore. The correct citation is: Riau AK, Wong TT, Lan W, Finger SN, Chaurasia SS, Hou AH, et al. (2011) Aberrant DNA Methylation of Matrix Remodeling and Cell Adhesion Related Genes in Pterygium. PLoS ONE 6(2): e14687. doi:10.1371/journal.pone. 0014687. The correct author contributions are: Conceived and designed the experiments: AKR TW LT. Performed the experiments: AKR SF SC SJY. Analyzed the data: AKR TW SF SSC AHH SC SJY LT. Contributed reagents/materials/analysis tools: TW WL SSC LT. Wrote the paper: AKR WL LT.
A new antibiotic, AM-2504.

In the course of screening for new alkaloids from microorganisms," a basic compound was isolated from the culture broth of the soil isolate, Streptomyces sp. strain No. AM2504. Later, it was found that this compound is a new peptide antibiotic. The sporophore of strain No. AM-2504 was spiral, representa tive of the section Spirales of Pridham et al.'' and the spore was oval with a smooth surface. The aerial mass color was gray and melanoid pigment did not form. A 48-hr culture of strain No. AM-2504 was transferred into 75 liters of medium in a 100liter fermentor and the fermentation was carried out for 2 days at 27°C. The composi tion of the seed medium was 2 % glucose, 0.5 peptone, 0.5 % meat extract, 0.3 % dried yeast, 0.3 % CaCO3 (pH 7 before sterilization). The production medium contained 1 glucose, 2 % starch, 0.5 % yeast extract, 0.5 peptone and 0.4% CaCO3 (pH 7 before steri lization). The titer of antibiotic AM-2504 was determined as the maximum dilution number of a Dragendorff positive solu tion. ' The culture broth was adjusted to pH 10 with aqueous ammonia. The antibiotic AM-2504 produced was extracted with 18 liters n-butyl acetate and then transferred into 1. 5 liters 0.1 N hydrochloric acid. The water layer was subsequently adjusted to pH 10 with aqueous ammonia and extracted twice with 1.2 liters of ethyl acetate. The combined extracts were dried over anhydrous sodium sulfate and concentrated in vacuo to dryness to yield 3.6 g of a yellowish brown powder. The crude powder was dissolved in chloroform and then chromatographed on silica gel (100 g) eluting with a solvent mixture of chloroform and methanol (100: 1, v/v). The active frac tions were concentrated in vacuo to yield 1.3 g of a yellowish powder. The yellowish
Comparison between in vitro and in vivo methods to screen iron bioavailability

An enhanced in vitro method to screen iron bioavailability (Fe-BA) was compared with an in vivo human method. Two recipes, previously evaluated in vivo for Fe-BA, were replicated and fed to an in vitro system. The first, a semi-synthetic meal, tested the effect of ascorbic acid on iron absorption. The second, a corn-bean meal, assessed in three experiments, the effect of Na2EDTA plus ferrous fumarate and the effect of FeSO4 and NaFeEDTA fortificants on iron absorption. For the first recipe, the in vitro and in vivo results were highly correlated (r = 0.9765; P = 0.0008). For the second recipe, the in vitro method displayed a similar trend to the in vivo results vis-à-vis ferrous sulfate and NaFeEDTA, but not ferrous fumarate plus Na2EDTA. This method is appropriate for rapid screening of a large number of samples prior to human evaluations; it uses less samples, reagent and supplies than a previous in vitro method.
Sequential movement into coastal habitats and high spatial overlap of predator and prey suggest high predation pressure in protected areas

In theory, predators should attempt to match the distribution of their prey, and prey to avoid areas of high predation risk. However, there is a scarcity of empirical knowledge on predator and prey spatial use when both are moving freely in their natural environment. In the current study, we use information collated on a predators' diet, its population structure, as well as predator and prey relative abundance, and track the movements of predator and prey simultaneously to compare habitat use and evaluate predation pressure. The study was conducted in elasmobranch protected areas of coastal Tasmania, Australia. The species considered were the broadnose sevengill shark Notorynchus cepedianus, the apex predator in the area, and five chondrichthyan prey species. Notorynchus cepedianus and its prey show similar seasonality in the use of these coastal areas: more abundant in warmer months and absent in winter. Predator and prey also showed high spatial overlap and similar habitat use patterns. These similar movement patterns of predator and prey combined with the additional ecological information (diet, population structure of predator, relative abundance of predator and prey) suggests that N. cepedianus move into coastal areas to exploit seasonally abundant prey. Also, while in protected areas, chondrichthyans are subjected to high predation pressure. Overall, results illustrate the value of simultaneously recording and integrating multiple types of information to explore predator–prey relationships and predation pressure.
High‐throughput respiration screening of single mitochondrial substrates using permeabilized CHO cells highlights control of mitochondria metabolism

Respiration analysis using isolated mitochondria and electrochemical oxygen sensing has contributed significantly to the knowledge about mitochondrial metabolism, which is involved in energy generation but also in ageing and numerous diseases. Here, we present a high‐throughput respiration screening for functional in situ mitochondrial studies in permeabilized Chinese hamster ovary cells. The determination of oxygen uptake rates allowed a quantitative comparison between different conditions and a distinction of substrates into three groups providing an insight into tricarboxylic acid (TCA) cycle regulation. The mitochondrial metabolization of citrate, isocitrate, glutamine, and glutamate was highly stimulated by ADP supply. In contrast, the metabolization of α‐ketoglutarate, succinate, fumarate, and malate was little controlled by the energy and redox state. Metabolization of pyruvate was very strictly regulated by several independent mechanisms: phosphorylation, feedback inhibition, but also by the availability of CoA. A moderate stimulation of pyruvate metabolization was accomplished by feeding both pyruvate and aspartate simultaneously. The presented high‐throughput respiration screening provides comprehensive information about the effect of single or mixed substrates on mitochondrial metabolic activities, including transport and TCA cycle regulation, and metabolic bottlenecks. This supports the design of efficient mammalian producer strains or feeding strategies, but also the investigation of pathological and toxicological effects related to mitochondrial metabolism.
Competition between two Sphagnum species under different deposition levels

Abstract Sphagnum magellanicum Brid. and Sphagnum fallax (Klinggr.) Klinggr. react differently to several nutrient applications. S. fallax is significantly promoted by additional nitrate and ammonium in the hollows and partly in the lawns while no positive effects of these treatments on S. magellanicum could be detected. On the hummocks nitrate and to a lesser extent ammonium reduces the growth of both species. Under lower than recent input levels the growth rates of both species decrease, indicating that the growth of these Sphagnum species used to be N limited in bogs. S. fallax can be characterized as a competitive species while S. magellanicum exhibits a stress-tolerant strategy. Under increased N deposition levels S. fallax is able to outcompete S. magellanicum in the hollows and if the water supply is sufficient also at lawn level. The atmospheric nitrogen supply may therefore be responsible for the present-day success of this species in the bog vegetation of central and north-eastern Europe.
Nonindigenous species introductions: a threat to Canada's forests and forest economy1

When organisms are moved from their natural range to new ecosystems, they are considered nonindigenous, invasive, or exotic species. Movement of exotic or native species may be international or from areas within Canada. Historically, Canada's forests have felt the effects of nonindigenous species introductions, as for example, Dutch elm disease, white pine blister rust, gypsy moth, and pine shoot beetle. With changes in global trade patterns, novel introductions will continue to occur. Although most of the research and regulatory efforts to control the movement of nonindigenous species has focused on insects, projects are underway to study fungal organisms and their association with insect vectors. International quarantine standards are being developed to minimize the risk associated with solid wood packing materials, a major entry pathway for nonindigenous organisms. Research needs include the development of enhanced detection capabilities, improved diagnostic tools, effective mitigation measures, as well as socio-economic impact assessments and basic biological information about nonindigenous species and their interactions with hosts.
New records of beaked whales, Genus Mesoplodon, from New Zealand (Cetacea: Ziphiidae)

Three species of beaked whales, Mesoplodon peruvianus, M ginkgodens and M densirostns, are newly recorded from New Zealand on the basis of stranded specimens M peruvianus was previously known from the eastern tropical Pacific, M ginkgodens from the sub‐tropical and tropical waters of the wider Pacific and equatorial Indian Oceans, and M densirostns from Australian and other warm temperate to tropical waters Diagnostic skull characters for the three species are discussed and illustrated Previous records of M ginkgodens from the Chatham Islands, and M densirostns from the east coast of New Zealand and Macquane Island, are incorrect
The partitioning of hydraulic conductances within mature orange trees

Sap flow (F) and leaf water potential (LWP) were followed diurnally in mature Valencia and Shamouti orange trees in an orchard. The hydraulic conductance of these trees was computed from the diurnal relationship between the LWP and F. The driving force for water movement was estimated from a weighted average of sunlit and shaded LWP, assuming that leaves in the shade transpire to some extent. LWP of covered, non-transpiring leaves was also measured hourly. It was assumed to represent the xylem water potential within the axial conduit of the trunk. Relating covered LWP to Fon an hourly basis enables the computation of the hydraulic conductance of the root system, including axial conductances. The hydraulic conductance of the transpiring crown was computed. Its magnitude was comparable to the root system hydraulic conductance.
Biomass allocation in old‐field annual species grown in elevated CO2 environments: no evidence for optimal partitioning

Increased atmospheric carbon dioxide supply is predicted to alter plant growth and biomass allocation patterns. It is not clear whether changes in biomass allocation reflect optimal partitioning or whether they are a direct effect of increased growth rates. Plasticity in growth and biomass allocation patterns was investigated at two concentrations of CO2 ([CO2]) and at limiting and nonlimiting nutrient levels for four fast‐ growing old‐field annual species. Abutilon theophrasti, Amaranthus retroflexus, Chenopodium album, and Polygonum pensylvanicum were grown from seed in controlled growth chamber conditions at current (350 μmol mol−1, ambient) and future‐ predicted (700 μmol mol−1, elevated) CO2 levels. Frequent harvests were used to determine growth and biomass allocation responses of these plants throughout vegetative development. Under nonlimiting nutrient conditions, whole plant growth was increased greatly under elevated [CO2] for three C3 species and moderately increased for a C4 species (Amaranthus). No significant increases in whole plant growth were observed under limiting nutrient conditions. Plants grown in elevated [CO2] had lower or unchanged root:shoot ratios, contrary to what would be expected by optimal partitioning theory. These differences disappeared when allometric plots of the same data were analysed, indicating that CO2‐induced differences in root:shoot allocation were a consequence of accelerated growth and development rates. Allocation to leaf area was unaffected by atmospheric [CO2] for these species. The general lack of biomass allocation responses to [CO2] availability is in stark contrast with known responses of these species to light and nutrient gradients. We conclude that biomass allocation responses to elevated atmospheric [CO2] are not consistent with optimal partitioning predictions.
TWO UNUSUAL AURICULARIOID FUNGI FROM NORWAY

Helicogloea caroliniana (Coker) G. E. Baker is described as new to Europe, based on collections in southwestern Norway. The parasitic species Achroomyces chlamydospora was found growing in the hymenium of H. caroliniana and is described as new to science.
Biochemistry and Molecular Biology of Soybean Seed Storage Proteins

ABSTRACT Soybean (Glycine max[L.] Merr.) is one of the principle field crops grown in the United States. From a crop with no significant economic value at the turn of this century, soybeans have made remarkable strides in U.S. agriculture, claiming the stature of the number two U.S. cash crop. Soybean is an important source of edible vegetable oil and protein throughout the world and is used in a multitude of food and industrial applications. Even though soybeans are a rich source of protein for livestock and humans, the nutritional quality of soybean proteins is not optimal. Some of the problems associated with soybean proteins include (1) presence of anti-nutritional factors such as trypsin inhibitor, (2) undesirable beany flavor, (3) elicitation of allergic reactions in susceptible individuals, (4) poor digestibility of soybean proteins, and (5) deficiency in sulfur-containing amino acids. As a consequence, concerted efforts are underway to improve the overall nutritive value of soybean proteins by both classical plant breeding and molecular biological approaches. This review article summarizes the current knowledge on the biochemistry and molecular biology of soybean seed storage proteins. Recent advances in the genetic improvement of amino acid composition of seed storage proteins are highlighted. The review also includes some recent achievements in modifying soybean seed composition.