Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved understanding of brain morphology through 3D printing: A brief guide

Brain morphology can provide insights into inter-individual differences. In the present guide, we outline the steps for generating a print-ready 3D model of brain structures from a standard T1-weighted structural MRI volume. By improving our understanding of brain morphology, we hope to enhance teaching and scientific communication, as well as aid in the development of novel measures of brain morphology.
SEXUAL SELECTION IN FEMALE PERCEPTUAL SPACE: HOW FEMALE TÚNGARA FROGS PERCEIVE AND RESPOND TO COMPLEX POPULATION VARIATION IN ACOUSTIC MATING SIGNALS

Abstract Female preferences for male mating signals are often evaluated on single parameters in isolation or small suites of characters. Most signals, however, are composites of many individual parameters. In this study we quantified multivariate traits in the advertisement call of the túngara frog, Physalaemus pustulosus. We represented the calls in multidimensional scaling space and chose nine test calls to represent the range of population variation. We then tested females for phonotactic preference between calls in each pair of the nine test calls. We used statistics developed for paired comparisons in such “round robin” competitions to evaluate the null hypothesis of equal attractiveness, and to examine the degree to which females responded to calls as being different from or similar to one another in attractiveness. We then examined the attractiveness of each test call relative to all other test calls as a function of their location in multivariate acoustic space (the acoustic landscape) to visualize sexual selection on calls. Finally, we used methods from cognitive psychology to illustrate the females' perception of call attractiveness in multivariate space, and compared this perceptual landscape to the acoustic landscape of quantitative call variation. We show that correlations between individual call characters are not strong and thus there are few biomechanical constraints on their independent evolution. Most call variables differed among males, and there was high repeatability of call characters within males. Females often discriminated between pairs of calls from the population, and there were significant differences among calls in their attractiveness. Female preferences for calls were not stabilizing. The region of the acoustic landscape that was most attractive to females included the mean call but was not centered around it. The females' perceptual or preference landscape did not correlate with the call's acoustic landscape, and female perception of calls decreased rather than enhanced call differences.
Participatory Disease Surveillance and Response in Indonesia: Strengthening Veterinary Services and Empowering Communities to Prevent and Control Highly Pathogenic Avian Influenza

Significance of Findings With the current prevalence of disease, the size of the poultry population, and the relatively poor zoo-sanitary standards within the poultry sector, it is now accepted that it will not be possible to gain control across all endemic areas within a short period of time. However, the risk of a H5N1 virus contributing to pandemic human influenza dictates that control must be achieved as quickly as possible. The enzootic nature of HPAI in Indonesia means that achieving sustainable disease control is going to be a difficult and long-term task. The PDSR program has made a significant contribution by involving communities and building capacity within the Animal Health Services and continues to be an important element of the fight against HPAI in Indonesia.
SEX-BIASED DISPERSAL IN A MIGRATORY BAT: A CHARACTERIZATION USING SEX-SPECIFIC DEMOGRAPHIC PARAMETERS

Abstract We studied the noctule bat (Nyctalus noctula), in which the mitochondrial FST is about 10 times that revealed by nuclear markers, to address two questions. We first verified whether random dispersal of one sex is compatible with highly contrasted mitochondrial and nuclear population structures. Using computer simulations, we then assessed the power of multilocus population differentiation tests when the expected population structure departs only slightly from panmixia. Using an island model with sex-specific demographic parameters, we found that random male dispersal is consistent with the population structure observed in the noctule. However, other parameter combinations are also compatible with the data. We computed the minimum sex bias in dispersal (at least 69% of the dispersing individuals are males), a result that would not be available if we had used more classical population genetic models. The power of multilocus population differentiation tests was unexpectedly high, the tests being significant in almost 100% of the replicates, although the observed population structure infered from nuclear markers was extremely low (FST = 0.6%).
New Insights into Photosynthetic Oscillations Revealed by Two-dimensional Microscopic Measurements of Chlorophyll Fluorescence Kinetics in Intact Leaves and Isolated Protoplasts¶

Abstract Chlorophyll fluorescence kinetic microscopy was used to analyze photosynthetic oscillations in individual cells of leaves and in isolated leaf cell protoplasts. Four Brassicaceae species were used: Arabidopsis halleri (L.) O'Kane & Al-Shehbaz, Thlaspi fendleri (Nels.) Hitchc, Thlaspi caerulescens J.&C. Presl and Thlaspi ochroleucum Boiss et Helder. With the latter two, the measurements were extended also to isolated protoplasts. The oscillations were induced under the microscope by exposing dark-adapted samples to actinic irradiance. Detailed analysis of the induced transients revealed that they consist of several processes oscillating with different frequencies and not only one component as reported earlier. Furthermore, it was found that most of these processes are controlled inside each individual cell. This was shown by differences in oscillations in neighboring cells and protoplasts that share a uniform intercellular environment. The frequency of the dominant oscillation frequency depended neither on irradiance nor on CO2 concentration and is, therefore, not controlled by the photosynthetic rate. Characteristic differences in the frequency spectrum and damping of oscillations have been found among the plant species examined.
Statistical Methods for Recommender Systems

Designing algorithms to recommend items such as news articles and movies to users is a challenging task in numerous web applications. The crux of the problem is to rank items based on users' responses to different items to optimize for multiple objectives. Major technical challenges are high dimensional prediction with sparse data and constructing high dimensional sequential designs to collect data for user modeling and system design. This comprehensive treatment of the statistical issues that arise in recommender systems includes detailed, in-depth discussions of current state-of-the-art methods such as adaptive sequential designs (multi-armed bandit methods), bilinear random-effects models (matrix factorization) and scalable model fitting using modern computing paradigms like MapReduce. The authors draw upon their vast experience working with such large-scale systems at Yahoo! and LinkedIn, and bridge the gap between theory and practice by illustrating complex concepts with examples from applications they are directly involved with.
Evaluation of Sunscreen Protection in Human Melanocytes Exposed to UVA or UVB Irradiation Using the Alkaline Comet Assay¶

Abstract The in vivo assessment of sunscreen protection does not include the photogenotoxicity of UVA or UVB solar radiation. Using the comet assay we have developed a simple and rapid technique to quantify sunscreen efficacy against DNA damage induced by UV light. Cutaneous human melanocytes from primary cultures were embedded in low-melting point (LPM) agarose and exposed to UVA (0.8 J/cm2) or to UVB (0.06 J/cm2) through a quartz slide covered with 10 μL volumes of sunscreens. DNA single-strand breaks induced directly by UVA at 4°C and indirectly through nucleotide excision repair by UVB following a 35 min incubation period at 37°C were quantified using the comet assay. Tail moments (TM) (tail length × %tail DNA) of 100 cells/sample were determined by image analysis. DNA damage was evaluated with a nonlinear regression analysis on the normalized distribution frequencies of TM using a χ2 function. The coefficients of genomic protection (CGP) were defined as the percentage of inhibition of DNA lesions caused by the sunscreens. Twenty-one sunscreens were evaluated, and the calculated CGP were compared with the in vivo sun protective factor (SPF) and with the protection factor UVA (PFA). Nonlinear relationships were found between SPF and CGPUVB and between PFA and CGPUVA.
CHARACTERIZATION OF ESCHERICHIA COLI ISOLATES FROM PERITONITIS LESIONS IN COMMERCIAL LAYING HENS

Five clinically normal chickens from three farms (farm A, farm B, and farm C), for a total of 15 clinically normal chickens, were examined bacteriologically. In a similar manner, five dead chickens with lesions of peritonitis from each of the same three commercial egg-laying operations were selected for bacterial culturing. Escherichia coli were isolated from the cloaca in 14 of 15 healthy chickens and from all 15 chickens with peritonitis. Oviducts of normal chickens did not contain E. coli (0/15) whereas oviducts from 13 of 15 hens with peritonitis were positive for this pathogen. No lesions and no E. coli (0/15) were found in the peritoneal cavity of healthy hens, but peritonitis lesions from 13 of 15 dead chickens yielded E. coli. On farm A and farm B, a flock consisted of all chickens within a single house and all chickens in each flock were of the same age and same genetic strain. In flock 1 from farm A, all five E. coli isolates from the oviduct and all five isolates from the peritoneal cavity were serogrouped as O78; contained the virulence genes iroN, sitA, iutA, tsh, and iss; and belonged to phylogenetic group A. In flock 2 from farm B, all four E. coli isolates from the oviduct and all four isolates from the peritoneal cavity were serogrouped as O111; contained virulence genes iroN, sitA, iutA, traT, iss, and ompT; and belonged to phylogenetic group D. These data suggest that all chickens with peritonitis in a single flock on farms A and B were likely infected by the same E. coli strain. Escherichia coli isolates from the magnum and peritoneum had the same serogroup, virulence genotype, and phylogenetic group, which is consistent with an ascending infection from the oviduct to the peritoneal cavity.
SURVEY FOR INFECTIOUS DISEASE IN THE SOUTH AMERICAN FUR SEAL (ARCTOCEPHALUS AUSTRALIS) POPULATION AT PUNTA SAN JUAN, PERU

The Peruvian population of the South American fur seal (Arctocephalus australis) is a distinct evolutionarily significant unit that is endangered. One of the largest rookeries for this species in Peru is located within the Punta San Juan marine protected area (158229S, 758129W). To better understand the current health status of this population, exposure to 10 pinniped pathogens was evaluated in adult female fur seals (n1⁄4 29) via serology and polymerase chain reaction (PCR) techniques in November 2010. The results suggest this population is naı̈ve to canine and phocine distemper viruses (serum neutralization test), five Leptospira interrogans serovars (microscopic agglutination test), and Brucella canis (card test). Indirect fluorescent antibody testing for Toxoplasma gondii, Neospora caninum, and Sarcocystis neurona was also uniformly negative. PCR testing of nasal swabs using previously described Mycoplasma spp. primers was positive in 37.9% (11/29) of samples. One animal was positive via card test for Brucella abortus, whereas 53.7% (15/28) were positive or suspect using a marine Brucella competitive enzyme-linked immunosorbent assay. Antibody to phocine herpesvirus-1 (PHV-1) was identified in 85.7% (24/28) of the sampled population by serum neutralization testing. Overall, exposure to Mycoplasma spp. , Brucella spp. , and PHV-1 was observed, but results demonstrated low to no exposure to many key pinniped pathogens. The expansion of human populations, agriculture, and industry along the Peruvian coast may lead to increased pathogen exposure from human, domestic, and wild animal sources. The naı̈ve nature of this key population of South American fur seals raises concerns about potential risk for disease outbreaks.
Water Stress, Osmolytes and Proteins1

Abstract Organic osmolytes are small solutes used by cells of numerous water-stressed organisms and tissues to maintain cell volume. All known osmolytes are amino acids and derivatives, polyols and sugars, methylamines, and urea; unlike salt ions, most are “compatible,” i.e., do not perturb macromolecules. In addition, some stabilize macromolecules and are “counteracting” towards perturbants, e.g., methylamines can stabilize proteins and ligand binding against perturbations by urea in elasmobranchs and mammalian kidney, and (our latest findings) high hydrostatic pressure in deep-sea animals. Methylamines appear to coordinate water molecules tightly, resulting in osmolyte exclusion from hydration layers of peptide backbones. This makes unfolded protein conformations entropically unfavorable (work of Timasheff, Galinski, Bolen and coworkers). These properties have led to proposed uses in biotechnology, agriculture and medicine, including improved biochemical methods, in vitro rescue of misfolded proteins in cystic fibrosis and prion diseases (work of Welch and others), and plants engineered for drought and salt tolerance. These properties also explain some but not all of the considerable variation in osmolyte composition among species with different metabolisms and habitats, and among and within mammalian tissues in development.
Heterogeneity of Diffusion Inside Microbial Biofilms Determined by Fluorescence Correlation Spectroscopy Under Two-photon Excitation¶

Abstract Fluorescence correlation spectroscopy (FCS) under two-photon excitation was applied successfully to characterize the penetration and diffusion capabilities of fluorescent probes (latex beads and fluorescein isothiocyanate–dextran) of different size and electrical charge in two models of monomicrobial biofilms with low (Lactococcus lactis biofilm) or high (Stenotrophonas maltophilia biofilm) contents of extracellular polymeric substance (EPS). FCS measurements performed on each biofilm can show deviation from Brownian diffusion, depending on the local structure of the biofilm and the fluorophore size. In this case, we fitted the data to an anomalous diffusion model and determined apparent diffusion coefficients, which can be 50 times smaller than the values in aqueous solutions. This result was interpreted as steric hindrance of the diffusion of the fluorescent particles within the biofilm that can lead to a total inhibition as observed particularly in the mushroom-like structure of the S. maltophilia biofilm. Alternatively, mechanisms for the absence of FCS signal behavior were related to attractive electrostatic interactions between cationic particles and negatively charged bacteria or to specific interactions between dextrans and EPS of the biofilm matrix.
EXTRAORDINARY MULTILOCUS GENETIC ORGANIZATION IN MOLE CRICKETS, GRYLLOTALPIDAE

Abstract Allozymic diversity at 21 loci was analyzed in 470 individuals of three species of mole cricket superspecies, Gryllotalpa gryllotalpa (two new chromosomal species, G. tali and G. marismortui) and G. africana in Israel, which are distributed along a southward transect of increasing aridity. Two outstanding findings emerged in G. tali and G. marismortui: (1) genetic polymorphism was high but heterozygosity very low, indicating significant deviations from Hardy-Weinberg expectations; and (2) significant linkage disequilibria at an unprecedented level for outbreeders and remarkable intersite differences. The results may characterize subterranean gryllotalpids worldwide because a single sample of Neocurtilla hexadactyla from Tefé, Amazonia, shows the same features. Significant variation of heterozygote paucity among loci, combined with the biology of the species, rejects the simple explanation of inbreeding or any other single explanatory model. Likewise, direct selection against heterozygotes or specific multilocus associations can explain, but is not necessary nor likely to explain, the observed results in mole crickets. To explain these results, we developed a multiple-factor mathematical model combining niche viability selection, niche choice, and positive assortative mating. This model involves a special case of Wahlund effect and inbreeding. Simulations based on this model showed that a combination of these three mechanisms may produce the observed distribution of alleles, via selection on a few loci, to affect the entire genome organization. Corresponding Editor: B. Bowen
Taxonomic Reevaluation of the Polylepis sericea Complex (Rosaceae), with the Description of a New Species

Abstract The taxonomically difficult genus Polylepis (Rosaceae) contains several problematic species complexes, including one around P. sericea. We here reevaluate species boundaries in this complex based on morphological characters and climatic niches. We recognize five species within the P. sericea complex, based primarily on leaf characters: P. albicans (northwestern Peru), P. argentea (central Peru) described here, P. canoi (southeastern Peru to central Bolivia), P. ochreata (Ecuador to southernmost Colombia), and P. sericea (Venezuela to central Colombia). We provide full synonymy, diagnostic notes, lists of selected specimens examined, and a key to the species of the complex.
Gas Exchange, MRS and NIRS Assessment of Metabolic Transients in Skeletal Muscle1

Abstract The study of the kinetics of O2 consumption (V̇o2) at the onset and offset of constant-load submaximal exercise (V̇o2 on- and off-kinetics) is useful from a practical point of view (a faster adjustment of oxidative metabolism following an increased metabolic demand reduces the need for substrate level phosphorylation, with implications on exercise tolerance and muscle fatigue) and can give valuable insights into the regulation of oxidative metabolism in skeletal muscle. Measurements have been carried out both in man and in animals, at the tissue and at the whole body level. At the tissue level, the V̇o2 on- and off-kinetics were determined: a) Directly, by dynamic solution of the Fick equation throughout the transients; attempts were also made to obtain similar informations by near-infrared spectroscopy. b) Indirectly, from the kinetics of phosphocreatine hydrolysis and resynthesis, by chemical methods or by 31P magnetic resonance spectroscopy. At the whole body level, V̇o2 on- and off-kinetics are determined from breath-by-breath measurements of pulmonary gas exchange. The V̇o2 = f(t) function is a complex one, particularly during the on-transient. The so-called “phase 2” of the V̇o2 on-response, as well as the V̇o2 off-response, yield relevant metabolic informations. In muscle the V̇o2 on- and off-kinetics are characterized by half-times (t½) of 15–20 sec. At the whole-body level, t½ of the V̇o2 on-kinetics show a wider variability, related to the experimental protocol and to other factors. The V̇o2 off-phase is more constant, and its kinetic parameters appear closer to those obtained at the tissue level. The study of the V̇o2 kinetics is valuable for a functional evaluation of skeletal muscle oxidative metabolism. In ordinary conditions muscle V̇o2 kinetics appears mainly imposed by intrinsic (metabolic) rather than extrinsic (O2 delivery) factors.
The design of a portable fetal heart rate and uterine contraction monitor

A new portable fetal heart rate (FHR) and uterine contraction (UC) monitor has been developed. The system is portable, light weight, small size, battery powered. It provides a predetermined "long-term" monitoring, and stores abnormal data. Only one 9 V commercial battery is used for the whole system, so it could be used safely by the high risk pregnant woman to monitor the abnormal FHR and UT activities, when she is not in the hospital. When the microprocessor-based system detects a predetermined "long-term" abnormal activity, it can activate the appropriate alarm to advise the pregnant woman to go to hospital as soon as possible. The abnormal data from the monitor are not transmitted to the hospital's personal computer till the pregnant woman receives medical treatment. A PC-based software to display the long-term abnormal FHR and UT data from the portable monitor by using window figures or graphs has also been provided, and these figures could help clinical doctors make diagnoses.
Measurement Method for Space Networks Authenticated Key Security under Distributed CA

The key management schemes bsaed on Distributed Certificate Authority resolve the difficulty to adopting concentrating key management in space networks,but result in some new threats of authenticated key.Based on discribing and analyzing the threats suffered by authenticated key of space networks,a measurement method for security intensity of authenticated key is proposed.The method can quantitatively measure the security intensity of authenticated key according to the setting of parameters,such as threshold value,key-update period etc.By analyzing the impact of threshold value and key-update period on authenticated key security,a method of setting the two networks security parameters reasonably is given.
Ultraviolet Inactivation of Feline Calicivirus, Human EntericViruses and Coliphages¶

Norwalk and Norwalk-like viruses (NLV) are major causes of foodand water-related disease in the United States. There is no host cell line in which the NLV can be tested for infectivity. Feline calicivirus (FCV) and NLV both belong to the family Caliciviridae. FCV can be assayed for infectivity in the Crandell Reese feline kidney cell line, so FCV serves as a surrogate for NLV. This study is the first report of UV inactivation of FCV and also of using the plaque technique, in contrast to the 50% tissue culture infectious dose end point technique, to determine the FCV infectivity titer. The infectivity titers (log10 plaque-forming units/mL) of UVinactivated FCV, hepatitis A virus (HAV), poliovirus type 1 (PV1) and two small, round coliphages were plotted as a function of UV dose and analyzed by regression analysis and analysis of variance. These fitted straight-line curves represent exponential inactivation, so UV inactivation can be said to show ‘‘one-hit kinetics. ’’ The decimal inactivation doses of UV for FCV, HAV, PV1, MS2 and uX174 were 47.85, 36.50, 24.10, 23.04 and 15.48 mW s/cm, respectively. FCV appears to be the most UV resistant among the tested viruses.