Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of rapid gene expression analysis and its application to bioprocess monitoring

Cultivation of a microorganism in a bioreactor offers an ideal environment for optimized production of industrial compounds and for studying biological phenomena under reproducible conditions. In order to be able better to understand and control biological systems both for industrial and scientific purposes, development of methods that generate more detailed information about the biosystems is required. The focus in the development of tools for monitoring and control of bioreactor cultivations is on analyses that report on the physiological status of the production organism. Genetic expression is an important and growing aspect of cellular physiology, because the genomic sequences are becoming available for an increasing number of organisms. Technologies enabling studies of whole genome-wide expression analysis have provided large quantities of gene expression data under various conditions. One consequence of this has been the discovery of smaller sets of genes that provide the essential information about the biological system of interest. This has increased the need for technologies enabling rapid and cost-effective detection of specific gene transcripts. The aim of the present study was to develop methods suitable for expression analysis of defined gene sets in bioprocess conditions, and to apply the methods for monitoring microbial cultures. The environmental conditions in bioreactor cultivations set certain challenges for the methodology. The environmental surroundings are typically in constant change during bioprocesses, requiring frequent analysis. In addition, the conditions are affected by various factors, such as decreasing nutrient and oxygen levels and increasing levels of secreted proteins or ethanol. Thus the number of relevant genes to be monitored in a process is dozens to hundreds rather than a few. For control purposes the response time of the method should be short.
Control Policy and Sustainability for Decision-Making in Asset Management

The essential factor determining decision-making in private investors and public corporations is controlled asset management. In a developed asset allocation and in a time of debt crisis, an important issue on which investors base their decisions is when and how to more or fewer investments such that expected net values of assets are maximized with minimal risks for sustainability in the management of capital assets. The acknowledgement of this enables investors to make rational decisions. The aim of this paper is to provide control policy to help investors make necessary decisions for sustainability in asset management. This is done by applying an optimal control model to a real-life problem asset-liability, thus derive the control policy .
Variation in the population distribution of two species of Tenuipalpid mites on their specific host medicinal plants

The Tenuipalpid mites are referred to as false spider mites or flat mites and the genus Brevipalpus is recognized as the economically most important group of species of Tenuipalpidae. It is becoming increasingly evident that they are potentially serious plant pests especially with their involvement as vectors of plant viruses. The objective of the present work is to study the variation in the population distribution of two species of Tenuipalpid mites, viz. Brevipalpus obovatus and Brevipalpus phoenicis on their specific host medicinal plants. A survey was conducted on the Phytophagous Tenuipalpid mites associated with medicinally important plants, viz. Ocimum sanctum, Ocimum gratissimum and Adhathoda vasica grown in Malappuram district of Kerala during the period of September to December in the year 2011. Results of the present survey indicated that the medicinal plants A. vasica and O. gratissimum were infested by B. phoenicis and the O. sanctum was infested by B. obovatus. The paper discusses on the population distribution of these Tenuipalpid mites on their specific host plants through Per Leaf Counting Method. To study the population distribution the number of various life stages, viz. adults, nymphal stages and eggs were recorded. Results of the survey enabled to reveal that the distribution of mite population was high in O. sanctum, moderate/medium in O. grattissimum and low in A. vasica. Feeding by theses mites leads to the collapse of the inner leaf tissue, and subsequently devitalizes the plant. Damage is characterized by browning of the damaged leaf surface. Quite often, infestation of the mite leads to leaf deformation also.
Cloning, sequencing, and expression of the pantothenate kinase (coaA) gene of Escherichia coli

Pantothenate kinase catalyzes the rate-controlling step in coenzyme A (CoA) biosynthesis. The structural gene (coaA) located at 90 min of the Escherichia coli chromosome was cloned and sequenced. The coaA gene was transcribed in the opposite direction to the flanking genes birA and thrU and produced a single 1.1-kb transcript. Translation of the coaA gene produced two protein products (36.4 and 35.4 kDa) that differed by eight amino acids at the amino terminus. The poor homology of the coaA promoter region to consensus E. coli promoter sequences and the low frequency of optimal codon usage (0.565) were consistent with the low abundance of pantothenate kinase. Strains containing multiple copies of the coaA gene possessed 76-fold-higher specific activity of pantothenate kinase; however, there was only a 2.7-fold increase in the steady-state level of CoA. These data corroborate the conclusion that regulation of pantothenate kinase activity by feedback inhibition is the critical factor controlling the intracellular CoA concentration.
Evaluation of molecular markers associated with resistance to late blight (Phytophthora infestans L.) in diploid and tetraploid potatoes

La papa, cultivo de importancia a nivel mundial es gravemente afectado por gota, enfermedad ocasionada por el oomy- cete Phytophthora infestans. Actualmente la forma más efectiva para combatir la enfermedad es mediante el desarrollo de cultivares resistentes al patógeno. Para esto, una estrategia es identificar genes que confieran resistencia al patógeno, para lo cual se buscan marcadores asociados con el carácter de resistencia. En este estudio se evaluaron marcadores moleculares tipo SCAR ( Sequence Characterized Amplified Region ): CosA, GP179, BA47f2 y Prp1 asociados con resistencia a P. infestans y el gen de resistencia R1, en 22 cultivares tetraploides pertenecientes a la subespecie andigena y cinco especies silvestres. Se evaluó el polimorfismo y se determinó si los alelos polimórficos permitían diferenciar genotipos resistentes de susceptibles. Se comparó el tamaño de los fragmentos obtenidos con los fragmentos esperados asociados con resistencia de acuerdo a reportes. El análisis se realizó considerando presencia/ausencia de los fragmentos: Abstract Potato is an important worldwide crop seriously affected by late blight disease caused by the oomycete Phytophthora in- festans . Currently, the most effective way to control the disease is developing resistant cultivars to the pathogen by identifying genes that confer resistance to the pathogen. For this purpose it is important to find molecular markers associated with the trait. In this study, the SCAR ( Sequence Characterized Amplified Region ) markers: CosA, GP179, BA47f2 y Prp1, associated with late blight and the resistant gen R1 were evaluated in 22 tetraploid cultivars from subspecie andigena and five wild potato species. Polymorphism was eva- luated and it was evaluated if polymorphic alleles allow differentiating resistant from susceptible genotypes. The fragment length for each marker was compared to the allele size reported associated to resistance. The analysis considered the pre- sence/absence of the fragments: CosA 210 , CosA 250, R1 1400, R1 BA47f2 , GP179 Prp1 Prp1 600 and Prp1 900 . The results indicated that both, tetraploid cultivars and wild potatoes, showed polymorphisms with all these markers, except with the GP179 marker. It was not found correlation between resistance and the presence of specific alleles. Evidence found in this study indicates that results obtained with molecular markers differed between tuberosum
Chemical accumulation and toxicological stress in three brown bullhead (Ameiurus nebulosus) populations of the Detroit River, Michigan, USA

Three populations of brown bullheads (Ameiurus nebulosus) were sampled in the Detroit River and analyzed for concentrations of persistent organic contaminants as well as incidences of external lesions and liver histopathology. Chemical analysis revealed that both the sediments and the bullheads of the Trenton Channel had the highest concentrations of organochlorine compounds, polychlorinated biphenyls, and polycyclic aromatic hydrocarbons compared with the other two sites (Amherstburg Channel and Peche Island). Furthermore, the Trenton Channel bullhead population had a higher prevalence of external abnormalities such as lip and skin lesions as well as truncated barbels. Histopathological analysis of the livers revealed higher prevalences of cholangiocarcinomas, cholangiomas, and other lesions in the Trenton Channel population. These observations support the conclusion that the health of the Trenton Channel bullhead population in the Detroit River is affected by exposure to organic chemicals, primarily through exposure to contaminated sediments.
Learning Manifold Dimensions with Conditional Variational Autoencoders

Although the variational autoencoder (VAE) and its conditional extension (CVAE) are capable of state-of-the-art results across multiple domains, their precise behavior is still not fully understood, particularly in the context of data (like images) that lie on or near a low-dimensional manifold. For example, while prior work has suggested that the globally optimal VAE solution can learn the correct manifold dimension, a necessary (but not sufficient) condition for producing samples from the true data distribution, this has never been rigorously proven. Moreover, it remains unclear how such considerations would change when various types of conditioning variables are introduced, or when the data support is extended to a union of manifolds (e.g., as is likely the case for MNIST digits and related). In this work, we address these points by first proving that VAE global minima are indeed capable of recovering the correct manifold dimension. We then extend this result to more general CVAEs, demonstrating practical scenarios whereby the conditioning variables allow the model to adaptively learn manifolds of varying dimension across samples. Our analyses, which have practical implications for various CVAE design choices, are also supported by numerical results on both synthetic and real-world datasets.
Efficacy of Natureseal® AS1 browning inhibitor in fresh-cut fruit salads applications, with emphasis on apple wedges

Summary Prevention of browning in fresh-cut fruit is of major commercial significance as fresh-cut fruit salads are major players in the international marketplace. Natureseal® AS1 and AS5 browning inhibitors out-performed ascorbic acid and citric acid in tests with fresh-cut wedges of ‘Bramley’ apple. A dipping regime of 2 min in 6% (w/v) AS1 solution was found to be optimal, as longer dip-times and higher concentrations led to significant residues of AS1 on the fresh-cut ‘Bramley’ wedges. Tests on fresh-cut wedges from ten apple cultivars indicated that AS1 was significantly beneficial (P < 0.001) to maintain wedge colour during chill-storage in all cultivars, with the exception of ‘Shampion’, which had a low browning tendency and performed equally well with or without AS1. Tests on the anti-oxidant status of a generic fruit salad, which was not treated with AS1 and stored for 15 d, indicated a significant reduction in anti-oxidant status, due largely to the depletion of vitamin C (from 137 to 97 mg 100 g−1 DW). Total phenolics contents remained relatively constant over the 15-d storage period. The outcomes from these trials have been presented to commercial food companies with a view to their uptake.
A new species of lizard of the Liolaemus elongatus clade (Reptilia: Iguania:Liolaemini) from Curi Leuvu River Valley, northern Patagonia, Neuquén, Argentina

A new species of the Andean-Patagonian Liolaemus elongatus clade is described. Liolaemus burmeisteri sp. nov. differs from other members of its clade in a character combination of light brown general coloration, plain dorsal pattern, dark lateral areas, a very bright orange-yellow coloration on femoral area and lower belly, and other morphological and genetic traits. It is distributed on a restricted area on sedimentary rocky outcrops found in an intermountain valley. Liolaemus burmeisteri sp. nov. is known only for its type locality in Curi Leuvu River Valley in northwestern Patagonia above 1037 m. A mitochondrial DNA gene tree analysis found this new species as the sister taxon of Liolaemus smaug .
BIOCHEMICAL INVESTIGATIONS ON RANA RIDIBUNDA PALL. AND RANA ESCULENTA L.

Our investigations pointed out the existence of a high variability of some biochemical indices in the hepatic, muscular and blood tissue at Rana ridibunda Pall. and Rana esculenta L. Higher amounts of sugars and transaminases were found in the tissues of Rana esculenta L. species, while Rana ridibunda Pall. was characterised by higher levels of fats (triglycerides and cholesterol). With some exceptions, the highest values of the analysed biochemical indices were found in blood. The electrophoresis of plasma blood proteins of the two species of green frogs showed the presence of 3  4 proteic fractions in blood. The albuminic fraction at Rana esculenta L. contains two sub-fractions, and this fact sustains the idea of a hybrid nature of this species.
Efficient Implementations of First-Order Steerable Differential Microphone Arrays With Arbitrary Planar Geometry

We present a spatial filtering approach to first-order steerable Differential Microphone Arrays (DMAs) with arbitrary planar geometry. In particular, the design of the spatial filter is based on a recently proposed frequency-domain design methodology that approximates, in a least-square sense, a target beampattern using the Jacobi-Anger expansion involving Bessel functions. Despite the generality of that approach, however, its computational cost turns out to be excessive when working with limited processing resources. The beamforming technique proposed in this manuscript overcomes this issue by exploiting the fact that in DMAs the spacing between sensors is typically smaller than the smallest wavelength of audio signals of interest. This allows us to substitute zero- and first-order Bessel functions with their Taylor series approximation truncated to the first order. Moreover, we show that this approximation allows us to derive an efficient discrete-time-domain implementation of first-order steerable differential beamformers based on arrays with arbitrary geometries.
Size, Return and Public Company's Performance: A Study Small and Large Companies on IDX During 3 Economic-Periods

The main objective of this research is descriptive analysis of stock return associated with firm size. The size of listed firms is classified into two main categories; small and large. The statistical results show that the size of firms have positive correlation with return, although the correlation level is relatively weak. This research was conducted during the period of year 2001 to 2014. From this research, it finds that large size firms yielded higher return than smaller ones, and also yielded higher risk. During the crisis period, both small & large firms yielded positive return, but large firms yielded higher return than smaller ones. During the pre-crisis and post-crisis period, both firms yielded positive return. This result is consistent with the findings during the in-crisis period where large firms yielded higher return than smaller firms. The implication of this research is investment portfolio in large firms is more profitable than smaller firms in any economic-cycle environment.
Effects of the colour and thickness of polyethylene film on ensiling conditions and silage quality of chopped maize, as investigated under ambient conditions and in mini‐silos

The influences of variations in thickness and colour of agricultural plastic film on silage preservation conditions and silage quality were investigated. Thirty cylindrical plastic containers (mini-silos; 0·3 m3) were filled with chopped maize and covered with five different types of film (90 µm white, 150 µm transparent, 150 µm white, 150 µm black, 200 µm white). Four mini-silos of each variant were placed in the open air, and two were housed and subjected to a test procedure. The maximum storage period of silages was 104 d. The surface temperature of the films was found to be strongly dependent on the type of sheet. The temperatures inside the mini-silos directly under the film differed significantly, whereas this effect was not recorded in the centre of the mini-silos. In all, the differences were quantitatively small. Results of the chemical analysis of silages did not reveal any significant influence of film type. This was also the case when restricting the analysis to the uppermost silage layer. These findings are discussed against the background of the relatively small temperature differences and likely effects on gas permeability. On the basis of the results presented, it is concluded that, under the conditions of the experiment, well-preserved forage of high nutritive value can be produced with silo sheets of differing colour, as well as with those of reduced thickness. Adequate mechanical robustness has to be ensured, if there is a reduction in film thickness.
Cell-cell recognition inyeast: Isolation ofintact a-agglutinin from Saccharomyces kluyveri

The- heat-labile sexual agglutinin fromSac- charomyces kluyveri strain 17(a-agglutinin) hasbeenisolated inanapparently intact formfromwild-type andmnnl(gly- cosylation-defective) cells. Thewild-type agglutinin ispolydis- perse, duetovariable degrees ofglycosylation, andmigrates onnative gels withanapparent massof>400kDa,whereas under denaturing conditions itappears somewhat smaller. The mnnlagglutinin isalso heterogeneous buthasalower molec- ularmassduetothepresence ofshorter N-and0-linked polymannose chains. Bothagglutinins areconverted sequen- tially byproteolysis toactive fragments of=450and60kDa, buttherateofproteolysis ofthemorehighly glycosylated wild-type agglutinin ismuchslower thanthatofthemnnl agglutinin. The60-kDa fragment wasisolated byHPLCand found tocontain 46%carbohydrate asmannose, allofwhich waslinked toserine andthreonine. Thus, theN-linked oligo- saccharides arerestricted tothat partoftheagglutinin mole- cule thatpresumably anchors theagglutinin inthecell wall. Whenhaploid cells ofopposite mating typeoftheyeast Saccharomyces kluyveri aremixed, theyagglutinate into clumps, anevent that isfollowed bythefusion ofpaired cells toformazygote (1). Thisprocess ismediated byspecies- specific agglutinins that areanchored intheyeast cell wall (2). InS.kluyveri, asinother species, theamating-type cell possesses anagglutinin that contains aheat-stable recogni- tion site that isreleased insoluble formbyreduction with dithiothreitol. Incontrast, thea-agglutinin isalarge manno- protein that isunaffected byreducing agents butisreadily denatured byheat. Studies onthea-agglutinin fromS.kluyveri strain 17 revealed that anactive component of60kDawasproduced byZymolyase digestion ofthecells (1). Subsequently, by using apurified 83-glucanase ofreduced proteolytic activity, Weinstock andBallou (3)obtained evidence foralarger active fragment of134kDathat appeared tobeformed from astill larger agglutinin molecule of>200kDa.Itwasfound that ahighly active protease intheZymolyase preparation degrades theintact agglutinin sequentially toactive frag- mentsof134and60kDa. Inthepresent report, aprotease-free 13-glucanase (4)has beenusedtorelease thea-agglutinin fromcells, andthe solubilized agglutinin waspurified byion-exchange andgel chromatography. Theagglutinins fromwildtypeanda glycosylation-defective mutantofS.kluyveri (designated mnnl) (5)havebeencompared bymolecular size andfor sensitivity todigestion byendo-N-acetylglucosaminidase H (endo H)andOerskovia xanthineolytica protease (4).
Sensitivities in Satellite Lidar‐Derived Estimates of Daytime Top‐of‐the‐Atmosphere Optically Thin Cirrus Cloud Radiative Forcing: A Case Study

An optically thin cirrus cloud was profiled concurrently with nadir‐pointing 1,064 nm lidars on 11 August 2017 over eastern Texas, including NASA's airborne Cloud Physics Lidar (CPL) and space‐borne Clouds and Aerosol Transport System (CATS) instruments. Despite resolving fewer (37% vs. 94%) and denser (i.e., more emissive) clouds (average cloud optical depth of 0.10 vs. 0.03, respectively), CATS data render a near‐equal estimate of the top‐of‐atmosphere (TOA) net cloud radiative forcing (CRF) versus CPL. The sample‐relative TOA net CRF solved from CPL is 1.39 W/m2, which becomes 1.32 W/m2 after normalizing by occurrence frequency. Since CATS overestimates extinction for this case, the sample‐relative TOA net forcing is ~3.0 W/m2 larger than CPL, with the absolute value reduced to within 0.3 W/m2 of CPL due its underestimation of cloud occurrence. We discuss the ramifications of thin cirrus cloud detectability from satellite and its impact on attempts at TOA CRF closure.
Feeding potential of Coccinella septempunctata Linn. (Coccinellidae: Coleoptera) on mustard aphid, Lipaphis erysimi Kalt. and potato peach aphid, Myzus persicae Sulzer

Feeding potential of Lady bird beetle, Coccinella septempunctata (Linn.) was studied under laboratory conditions on mustard aphid, Lipaphis erysimi (Kalt.) and potato-peach aphid, Myzus persicae (Sulzer). Both grubs and adult showed greater preference for L. erysimi than M. persicae. The feeding potential of C. septempunctata increased with the increase in age of the grubs. Fourth instar grub consumed 69.40 and 61.50 aphids of L. erysimi and M. persicae respectively. The mean consumption of aphids, L. erysimi and M. persicae by unstarved stages was 43.28 and 36.56 respectively, while it was 58.85 and 51.10 under starved conditions.
Are adult amateur musicians at ‘high risk’ of experiencing musculoskeletal symptoms?

Musculoskeletal symptoms (MSSs) are a common problem for musicians, but the MSS burden of amateur musicians specifically is under-investigated. For the first time we sought to compare the MSS prevalence and profile (e.g. MSS location, impact) of adult amateur musicians with those of non-musicians. Amateur and non-musicians were asked to complete a questionnaire that collected data on their demographics, musical activities and MSS outcomes. A total of 456 participants were included, 30.9% of whom were amateur musicians. MSSs were common for both amateurs and non-musicians (96.4% and 96.1%, respectively, for the last twelve months). The only significant difference between the two groups was for the twelve-month prevalence of head MSSs with amateur musicians having a higher prevalence than non-musicians (49.6% and 39.8%, respectively, p<0.05). We conclude that amateur musicians do not have a substantially different MSS prevalence and profile compared with non-musicians for this university-based population.