Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating single-tree attributes by airborne laser scanning: methods based on computational geometry of the 3-D point data

Airborne laser scanning (ALS) has become a very common forest inventory data source during the 2000’s. Previous research on single-tree interpretation of such data suggests limitations due to both undetected trees and inaccuracies in species recognition and allometric estimation of stem dimensions. This work examined reconstruction of tree crowns by means of computational geometry of the point data and techniques for turning the obtained crown shape and structure information into improved estimates of tree attributes. Alpha shape metrics, i.e. a collection of various volume, complexity and area features derived from 3-D alpha shapes based on the point data, were found to have potential for describing species-specific allometric differences in the trees, while combining these metrics with features based on the height and intensity distributions in the data was beneficial with respect to the final accuracies. Nearest neighbor estimation proved efficient for making use of the high number of predictors available, but also for the simultaneous estimation of the attributes of interest, thus avoiding error propagation of an estimation chain. Random Forest, in particular, proved to be a flexible method with an ability to handle all available predictors with no need for their reduction. The classification of dominant to intermediate Scots pine, Norway spruce and deciduous trees showed an accuracy of 78%, and the estimates of diameter at breast height, tree height, and stem volume had root mean square errors of 13%, 3%, and 31%, respectively, when evaluated against separate validation data. Less supervised tree detection and estimation resulted in unreliable tree-level descriptions of the test stands, being hindered by both inaccuracy in the tree attributes, especially in species identification, and errors in tree delineation. The need to acquire field reference data and a potential need for an auxiliary information source both place constraints on the applicability of the developed approach. On the other hand, it was shown that crown base height, which is an important measure of external quality of mature Scots pine trees, could be estimated with an RMSE of 20–30% solely by ALS data with a pulse density of 4 m. The results suggest focusing single-tree interpretation specifically towards detailed measurements on the dominant tree layer, thus presenting a further need to assess the tree-level production line with respect to obtainable information, alternative methods and their costs.
Mechanisms Associated with the Negative Inotropic Effect of Deuterium Oxide in Single Rat Ventricular Myocytes

Deuterium oxide (D2O) is known to cause a negative inotropic effect in muscle although the mechanisms associated with this response in cardiac muscle are not well understood. We studied the effects of D2O in single rat ventricular myocytes in order to characterise the mechanisms associated with its negative inotropic effect and to assess its possible use as an acute modulator of microtubules. D2O rapidly reduced the magnitude of contraction in rat ventricular myocytes, and there was some recovery of contraction in the presence of D2O. Colchicine, an agent known to depolymerise microtubules, did not modify the effect of D2O. D2O decreased the L‐type Ca2+ current (ICa), measured under whole cell and perforated patch clamp conditions. Slowing of the time to peak and a delay in inactivation of ICa were observed. Intracellular calcium ([Ca2+]i) and sodium ([Na+]i) were measured using the fluorescent indicators fura‐2 and SBFI, respectively. The fall in contraction upon exposure to D2O was not associated with a fall in the [Ca2+]i transient; this response is indicative of a reduction in myofilament Ca2+ sensitivity. Both the [Ca2+]i transient and [Na+]i increased during the partial recovery of contraction in the presence of D2O. We conclude that a decrease in the myofilament sensitivity for Ca2+ and a reduction in Ca2+ influx via ICa are principally responsible for the negative inotropic effect of D2O in cardiac muscle. We found no evidence to explain the negative inotropic effect of D2O in terms of microtubule proliferation. In addition we suggest that acute application of D2O is not a useful procedure for the investigation of the role of microtubules in excitation‐contraction coupling in cardiac muscle.
Lens defects in Astyanax mexicanus Cavefish: Evolution of crystallins and a role for alphaA‐crystallin

The fish Astyanax mexicanus presents, within the same species, populations of river‐dwelling surface fish (SF) and blind cave‐living fish. In cavefish (CF), the eyes develop almost normally during embryogenesis. But 40 h after fertilization, the lens enters apoptosis, triggering the progressive degeneration of the entire eye. Before apoptosis, the CF lens expresses early differentiation factors correctly. Here, we searched for possible late differentiation defects that would be causal in CF lens degeneration. We reasoned that crystallins, the major lens structural proteins, could be defective or misregulated. We surveyed the CF and SF transcriptomes and uncovered 14 Astyanax crystallins from the beta, gamma, lambda, mu, and zeta families. These proteins are less polymorphic and accumulate more fixed mutations, some at highly conserved positions, in CF than in SF, suggesting relaxed selection at these loci in CF. In situ hybridizations and qPCR show that crybb1c, crybgx, crygm5 are expressed at much lower levels or are not expressed in the CF lens. For the best crystallin candidates, we tested a potential causal role in CF lens apoptosis. Crybgx, crybb1c (not expressed in CF from very early on), and cryaa (previously shown to be faintly expressed in CF) failed to induce any defect when knocked‐down in zebrafish embryos. However, the anti‐apoptotic cryaa protected lens cells from apoptosis when reexpressed by transgenesis in CF, suggesting a cell‐autonomous effect of cryaa on lens cell survival. Altogether, these data suggest that crystallin sequence evolution and expression defects may contribute to the loss of eyes in CF. © 2014 Wiley Periodicals, Inc. Develop Neurobiol 75: 505–521, 2015
A comparison of fluorescent in situ hybridization and multiplex short tandem repeat polymerase chain reaction for quantifying chimerism after stem cell transplantation.

BACKGROUND AND OBJECTIVES Despite the great utility of chimerism analysis after allogeneic stem cell transplantation, a gold standard method for its quantification has not yet been defined. The objective of the present investigation was to compare the sensitivity (detection limit) and the quantification accuracy of fluorescent in situ hybridization with specific probes for the sex chromosomes (XY-FISH) and multiplex short tandem repeat polymerase chain reaction (STR-PCR) revealed by capillary electrophoresis for the quantification of chimerism after stem cell transplantation. DESIGN AND METHODS A first experiment was performed on two sets of artificial cell mixtures from two sex-mismatched healthy donors mixed in different proportions (% male: 100, 75, 50, 25, 10, 5, 3, 1, 0.1, 0). In a second experiment, 58 samples obtained from 10 selected patients with different clinical courses and chimerism evolution after sex-mismatched stem cell transplantation, which had been studied by XY-FISH, were retrospectively analyzed by STR-PCR. In a third experiment, 60 unselected prospective samples belonging to 15 patients (5 of whom had also been included in the retrospective study) were analyzed by both XY-FISH and STR-PCR. RESULTS Both techniques showed high quantification accuracy and were highly reproducible. The sensitivity of both approaches reached 1% under standard conditions. Moreover, the use of long injection times for the capillary electrophoresis (30 and 50s vs. the standard 10s) resulted in an increase of sensitivity of the STR-PCR assay up to 0.1%, which has interesting clinical implications. INTERPRETATION AND CONCLUSIONS Considering the high sensitivity and quantification accuracy of multiplex STR-PCR and the fact that this assay is sex-independent and can be applied to virtually all patients, STR-PCR could be considered as the method of choice for chimerism quantification after stem cell transplantation when high sensitivity is not a requirement.
Outbreak of acute gastroenteritis associated with group A rotavirus and genogroup I sapovirus among adults in a mental health care facility in Japan

An outbreak of acute gastroenteritis consisting of 57 cases occurred in a mental health care facility in Takasaki city, Japan during 6th February and 27th March 2002. A total of 18 fecal specimens collected from 17 residents and one member of the medical staff during this outbreak were tested for the presence of viral enteropathogens by RT‐PCR and latex agglutination. Group A rotavirus and sapovirus were detected in 5 out of 18 fecal specimens (55.6%). To our knowledge, this is the first finding of an outbreak of gastroenteritis associated with co‐circulation of different kinds of viruses such as group A rotavirus and sapovirus. All of group A rotaviruses were typed further as P[4]G2 strains. Both rotavirus and sapovirus were subjected to molecular analysis by sequencing. It was noteworthy that all rotaviruses and sapoviruses had high homologies, respectively, to each other and sapoviruses presented a potential novel sapovirus genogroup I (GI) genotype, which was obviously different from any GI genotypes (GI‐a, b, c, and d). The outbreak associated with these viruses spread gradually from dormitory to dormitory, suggesting a spread by person‐to‐person contact, although investigation on the route of transmission of the outbreak is lacking. The findings confirm the presence of group A rotavirus and sapovirus are important in acute gastroenteritis among adults in Japan. J. Med. Virol. 75:475–481, 2005. © 2005 Wiley‐Liss, Inc.
Combined antiretroviral therapy and the incidence of acquired immunodeficiency syndrome–related central nervous system diseases

Controversial results of neuropathological studies assessing the effect of antiretroviral treatment on central nervous system (CNS) diseases have emphasized the need for longitudinal studies. A recent article published by d’Arminio Monforte and colleagues provides evidence of a decreased incidence of acquired immunodeficiency syndrome (AIDS) dementia complex (ADC) and other CNS diseases in a European cohort of human immunodeficiency virus (HIV)–infected individuals between 1994 and 2002. The decrease, similar to that of non-CNS AIDS-defining illnesses, is almost completely explained by improved immunological conditions and inhibition of viral replication. Although the findings are convincing, this study has potential limits and biases, specifically, missing information on CNS diseases diagnosed after first AIDS-defining illnesses, short time of observation before the introduction of combined antiretroviral therapy, and lack of availability of HIV seroconversion dates. To confirm the results of the above-mentioned study, we repeated the analysis using data from the Italian Seroconversion Study, a cohort of individuals with known dates of HIV serconversion. Kaplan–Meier curves were used to estimate the risk of developing ADC and other CNS diseases (ie cerebral toxoplasmosis, cryptococcosis, progressive multifocal leukoencephalopathy, primary brain lymphoma) after HIV seroconversion (estimated as the midpoint in time between the last negative and first positive test), before and after the introduction of highly active antiretroviral therapy. Adjusted relative hazards (RHs) and their 95% confidence intervals (CIs) were obtained by multivariate Cox models, with calendar year used as dichotomous time-dependent variable, adjusting for age, sex, and transmission category. Overall, 2,045 individuals were enrolled. The median age was 27 years (range, 14–75); 70% were male subjects. During a median follow-up time of 9 years, 191 participants developed an event (78 ADC, 95 other CNS diseases, and 18 both). The incidence of CNS diseases decreased from 2.3 per 100 person-years in 1996 to 0.3 in 2001–02. The risk of developing any CNS disease at 10 years after HIV seroconversion was 0.15 (95% CI, 0.13–0.19) and 0.05 (95% CI, 0.04–0.07) before and after 1997, respectively. At the multivariate analysis (Table), the risk of developing ADC and/or any CNS disease decreased significantly since 1997 (tripletherapy era), whereas no effect was observed in 1995–96 (double-therapy era). In conclusion, we confirm the decline of the incidence of ADC and other CNS diseases, also when controlling for duration of HIV infection. The decline began after the introduction of triple therapy and has continued over the following years. The study was funded by “Programma Ricerche AIDS, Sottoprogetto Epidemiologia,” Istituto Superiore di Sanità.
Influence of quebracho tannins administration on some blood metabolites in sheep and goats

Eight Merino sheep (49.4±4.23 kg LW) and eight Alpine goats (53.2±2.51 kg LW) were used in two experiments to study the effect of quebracho tannins (Q) on some plasma metabolites. Four sheep and four goats were fed daily 20 g DM of alfalfa hay (3-5 cm) per kg LW (A), whereas the other animals were given the same amount of hay treated with 50 g of Q. Blood sample s were taken after 5, 34, and 64 days of start- ing the administration of the Q diet, to assay some plasma met abolites (i.e. alkaline phosphatase (ALP), gamma glutamyltransferase (GGT), glutamic oxaloacetic transaminase (GOT ), and creatinin) as indicators of liver and kidney function. The concentration of the above men tioned plasma metabolites was unaffected by the inclusion of quebracho in the diet for the three sampli
The Effects of Measurement Distance on the Broadside Symmetric Leaky Wave Antenna

The effects of measuring a symmetric broadside leaky wave antenna (LWA) at finite distances are examined. In particular, the broadside beam behavior near the beam splitting condition is studied since the directivity error can be significant. The patterns at various distances, including the rule of thumb distance of 2L2 / lambdao, are calculated and compared to the far-field (FF) pattern. In addition, variations in measurement error at the finite distances due to the sign of the leaky wave phase constant are identified.
Epigenetic Modulation of Gene Expression from Quiescent Herpes Simplex Virus Genomes

ABSTRACT The ability of herpes simplex virus to persist in cells depends on the extent of viral-gene expression, which may be controlled by epigenetic mechanisms. We used quiescent infection with the viral mutants d109 and d106 to explore the effects of cell type and the presence of the viral protein ICP0 on the expression and chromatin structure of the human cytomegalovirus (HCMV) tk and gC promoters on the viral genome. Expression from the HCMV promoter on the d109 genome decreased with time and was considerably less in HEL cells than in Vero cells. Expression from the HCMV promoter in d106 was considerably more abundant than in d109, and this increased with time in both cell types. The same pattern of expression was seen on the tk and gC genes on the viral genomes, although the levels of tk and gC RNA were approximately 102- and 105-fold lower than those of wild-type virus in d106 and d109, respectively. In micrococcal-nuclease digestion experiments, nucleosomes were evident on the d109 genome, and the amount of total H3 as determined by chromatin immunoprecipitation was considerably greater on d109 than d106 genomes. The acetylation of histone H3 on the d106 genomes was evident at early and late times postinfection in Vero cells, but only at late times in HEL cells. The same pattern was observed for H3 acetylated on lysine 9. Trimethylation of H3K9 on d109 genomes was evident only at late times postinfection in Vero cells, while it was observed both early and late in HEL cells. Heterochromatin protein 1γ (HP1γ) was generally present only on d109 genomes at late times postinfection of HEL cells. The observations of chromatin structure correlate with the expression patterns of the three analyzed genes on the quiescent genomes. Therefore, several mechanisms generally affect the expression and contribute to the silencing of persisting genomes. These are the abundance of nucleosomes, the acetylation state of the histones, and heterochromatin. The extents to which these different mechanisms contribute to repression vary in different cell types and are counteracted by the presence of ICP0.
The effect of glutamine supplementation on the function of neutrophils from exercised rats

In a recent publication, we showed the protective effect of glutamine on neutrophil apoptosis induced by acute exercise. The purpose of the present study was to examine the effect of a single bout of intensive exercise on rat neutrophil function and the possible effect of glutamine supplementation. An aqueous solution of glutamine was given by gavage (1 g per kg b.w.), 1 h before the exercise session. The exercise was carried out on a treadmill for 1 h at 85% VO2máx. Neutrophils were obtained by intraperitoneal lavage with PBS. The following parameters were evaluated: phagocytosis capacity, production of nitric oxide and reactive oxygen metabolites, expression of iNOS, and expression of NADPH‐oxidase components (p22phox, p47phox and gp91phox). One hour of exercise at 85% VO2max. induced no change in the phagocytosis capacity and reactive oxygen species production but decreased nitric oxide production. When rats received oral glutamine supplementation, the phagocytosis capacity was significantly increased, the decrease in nitric oxide production induced by exercise was abolished and production of reactive oxygen species was raised. Glutamine supplementation presents a significant effect on neutrophil function including changes induced by exercise. Copyright © 2004 John Wiley & Sons, Ltd.
Detection of Raspberry ringspot virus Using Reverse Transcription Loop-mediated Isothermal Amplification

Raspberry ringspot virus (RpRSV), which has not occurred in Japan, infects many plants such as raspberry, gooseberry, cherry, grapevine, and strawberry. Biological assay, enzyme-linked immunosorbent assay (ELISA), and reverse transcription polymerase chain reaction (RT-PCR) have been introduced for the detection of RpRSV in postentry quarantine in Japan. We studied reverse transcription loop-mediated isothermal amplification (RT-LAMP) for RpRSV detection. As a result, the detection limit in RT-LAMP that employed primers specific for RpRSV was more than 10 times as high as that in the RT-PCR. Furthermore, simple and rapid sample preparation methods were evaluated, and the virus detection time was able to be reduced compared to modified SDS‒Potassium acetate method.
In vitro determination of radiation sensitivity parameters for DU-145 prostate cancer cells

Purpose: The prolonged delivery times associated with intensity modulated radiation therapy (IMRT) may reduce treatment effectiveness of radiation therapy for cancers with short repair half-times. In this study, in vitro radiation experiments with DU-145 prostate cancer cells were designed to quantify the half-time of sublethal damage repair. Method and materials: A series of single-fraction and split-dose clonogenic survival experiments were performed and analyzed using the linear-quadratic (LQ) survival model with mono-/two-component exponential and reciprocal-time repair kinetic models. Results: Our data indicate that DU-145 cells are very radiosensitive (α = 0.44 Gy−1, standard CI: 0.41–0.49 Gy−1) and are relatively insensitive to dose fractionation (α/β = 16 Gy, standard CI: 12–34 Gy). The estimated repair half-time is 23 min (standard CI: 10–97 min) with some evidence that a small portion of the sublethal damage is repaired more slowly. Conclusion: The reported radiosensitivity parameters (α and α/β) are larger than those derived from other in vitro experiments and clinical data. In contrast, the half-time for sublethal damage repair (∼23 min) is close to the one derived from clinical data (∼16 min). For such short repair half-times, the effectiveness of IMRT treatments may be substantially improved by decreasing the fraction delivery time.
Proinflammatory and Th2-Derived Cytokines Modulate CD40-Mediated Expression of Inflammatory Mediators in Airway Epithelia: Implications for the Role of Epithelial CD40 in Airway Inflammation

Cytokines produced by activated macrophages and Th2 cells within the lung play a key role in asthma-associated airway inflammation. Additionally, recent studies suggest that the molecule CD40 modulates lung immune responses. Because airway epithelial cells can act as immune effector cells through the expression of inflammatory mediators, the epithelium is now considered important in the generation of asthma-associated inflammation. Therefore, the goal of the present study was to examine the effects of proinflammatory and Th2-derived cytokines on the function of CD40 in airway epithelia. The results show that airway epithelial cells express CD40 and that engagement of epithelial CD40 induces a significant increase in expression of the chemokines RANTES, monocyte chemoattractant protein (MCP-1), and IL-8 and the adhesion molecule ICAM-1. Cross-linking epithelial CD40 had no effect on expression of the adhesion molecule VCAM-1. The proinflammatory cytokines TNF-α and IL-1β and the Th2-derived cytokines IL-4 and IL-13 modulated the positive effects of CD40 engagement on inflammatory mediator expression in airway epithelial cells. Importantly, CD40 ligation enhanced the sensitivity of airway epithelial cells to the effects of TNF-α and/or IL-1β on expression of RANTES, MCP-1, IL-8, and VCAM-1. In contrast, neither IL-4 nor IL-13 modified the effects of CD40 engagement on the expression of RANTES, MCP-1, IL-8, or VCAM-1; however, both IL-4 and IL-13 attenuated the effects of CD40 cross-linking on ICAM-1 expression. Together, these findings suggest that interactions between CD40-responsive airway epithelial cells and CD40 ligand+ leukocytes, such as activated T cells, eosinophils, and mast cells, modulate asthma-associated airway inflammation.
A power efficient current-mode differential driver for FPGAs

This paper is committed to design a power efficient signal driver for high speed differential transmission in FPGAs. The current-mode differential driver can convert full swing differential signals to small swing differential signals with low power consumption and can transmit signals through a long distance without inserting buffers. The programmable delay elements in the driver guarantee that the driver can be adapted for different transmission lengths and different frequencies to get the best tradeoff between speed and power. The power down mode function can decrease the static current to 4.75nA. The simulation with load models shows that the circuit can operate at a frequency up to 2.5GHz with good integrity, when transmission length is 2.4mm.
Is Frozen-Section Diagnosis a Reliable Guide in Surgical Treatment of Stage I Endometrial Carcinoma?

Frozen-section diagnoses and paraffin-section diagnoses were compared in 154 patients in stage I endometrial adenocarcinoma. In 134 (87%) of the 154 patients (p < 0.001), a corresponding depth of myometrial invasion was found, and in 132 (85.7%) patients the same tumor grade was established (p < 0.001). Frozen-section diagnosis of stage I endometrial adenocarcinoma is reliable for estimation of the extent of disease and accurately identifies patients who require surgical staging.