Miracle-dz/UniFAR-FTUs huggingface dataset:
A Multiscale Method for Selecting Indicator Species and Priority Conservation Areas: a Case Study for Broadleaved Forests in Lombardy, Italy

Abstract: Our purpose was to define a quantitative and expeditious method to analyze the effects of processes that influence species distribution and abundance at different organizational scales. We considered habitat loss, the breaking apart of habitat patches, and habitat structural alteration critical processes that affect species distribution and abundance. We evaluated the effects of these processes by considering the response of selected indicator species to isolation (landscape scale), patch size and edge effect (patch scale), and habitat structure (plot scale). We used broadleaf forests as our case‐study ecosystem and birds as indicator species. Faunal data came from a georeferenced, long‐term, breeding‐bird database, and environmental data were obtained from field surveys and land‐use digital cartography. Birds, grouped according to their sensitivity to patch isolation, patch size, edge effect, and habitat structure, indicated how environmental conditions affected species abundance. The most sensitive group to the above‐mentioned processes included the Marsh Tit (Parus palustris), Nuthatch (Sitta europaea), and Short‐toed Treecreeper (Certhia brachydactyla). We evaluated the umbrella effect of these species for the conservation of the other co‐occurring birds and found that their effectiveness varied according to the criterion used to select sites for protection. Site selection based on indicator species identified forest patches with greater species abundance than an alternative criterion that chose sites based on patch isolation and size, edge effect, and forest structure. The alternative criterion, although not as efficient as indicator species, may nevertheless be useful and effective for conservation when faunal data are lacking and guidelines for habitat management or restoration are needed. Our method is applicable to other ecosystems and taxa because the processes we considered occur in many ecosystems and may have significant effects on species from all taxonomic groups.
Development and Preliminary Evaluation of a Motorized Needle Guide Template for MRI-Guided Targeted Prostate Biopsy

To overcome the problems of limited needle insertion accuracy and human error in the use of a conventional needle guide template in magnetic resonance imaging (MRI)-guided prostate intervention, we developed a motorized MRI-compatible needle guide template that resembles a transrectal ultrasound-guided prostate template. The motorized template allows automated, gapless needle guidance in a 3T MRI scanner with minimal changes in the current clinical procedure. To evaluate the impact of the motorized template on MRI, signal-to-noise ratio and distortion were measured under various system configurations. A maximum of 44% signal-to-noise ratio decrease was found when the ultrasonic motors were running, and a maximum of 0.4% image distortion was observed due to the presence of the motorized template. To measure needle insertion accuracy, we performed four sets of five random target needle insertions mimicking four biopsy procedures, which resulted in an average in-plane targeting error of 0.94 mm with a standard deviation of 0.34 mm. The evaluation studies indicated that the presence and operation of the motorized template in the MRI bore create insignificant image degradation, and provide submillimeter targeting accuracy. The automated needle guide that is directly controlled by navigation software eliminates human error so that the safety of the procedure can be improved.
Validity of PALMS GPS scoring of active and passive travel compared with SenseCam.

PURPOSE The objective of this study is to assess validity of the personal activity location measurement system (PALMS) for deriving time spent walking/running, bicycling, and in vehicle, using SenseCam (Microsoft, Redmond, WA) as the comparison. METHODS Forty adult cyclists wore a Qstarz BT-Q1000XT GPS data logger (Qstarz International Co., Taipei, Taiwan) and SenseCam (camera worn around the neck capturing multiple images every minute) for a mean time of 4 d. PALMS used distance and speed between global positioning system (GPS) points to classify whether each minute was part of a trip (yes/no), and if so, the trip mode (walking/running, bicycling, or in vehicle). SenseCam images were annotated to create the same classifications (i.e., trip yes/no and mode). Contingency tables (2 × 2) and confusion matrices were calculated at the minute level for PALMS versus SenseCam classifications. Mixed-effects linear regression models estimated agreement (mean differences and intraclass correlation coefficients) between PALMS and SenseCam with regard to minutes/day in each mode. RESULTS Minute-level sensitivity, specificity, and negative predictive value were ≥88%, and positive predictive value was ≥75% for non-mode-specific trip detection. Seventy-two percent to 80% of outdoor walking/running minutes, 73% of bicycling minutes, and 74%-76% of in-vehicle minutes were correctly classified by PALMS. For minutes per day, PALMS had a mean bias (i.e., amount of over or under estimation) of 2.4-3.1 min (11%-15%) for walking/running, 2.3-2.9 min (7%-9%) for bicycling, and 4.3-5 min (15%-17%) for vehicle time. Intraclass correlation coefficients were ≥0.80 for all modes. CONCLUSIONS PALMS has validity for processing GPS data to objectively measure time spent walking/running, bicycling, and in vehicle in population studies. Assessing travel patterns is one of many valuable applications of GPS in physical activity research that can improve our understanding of the determinants and health outcomes of active transportation as well as its effect on physical activity.
Corpus Callosum Volume and Interhemispheric Transfer in Multiple Sclerosis

Background: The corpus callosum (CC) is frequently compromised in patients with multiple sclerosis (MS). Structural and functional measurements of the CC may be useful to monitor the progression of the disease. The aim of this pilot study was to determine if bimanual tactile temporal thresholds correlates with CC volume. A tactile temporal threshold is the longest temporal interval that separates the onsets of two tactile stimuli when they are judged by the observer as simultaneous. Judgments to bimanual stimulations require interhemispheric transfer via the CC. Methods: Thresholds were examined in MS patients and matched controls. Magnetic resonance (MR) images were acquired on a 3T MR system within 48 hours of clinical assessment and measurement of thresholds. Results: Corpus callosum volume was assessed by using a semiautomatic livewire algorithm. The CC volume was smaller (by 21% on average, p < 0.01) and thresholds were higher (by 49% on average, p < 0.03) in MS patients when compared to controls. A significant correlation (r = -0.66, p = 0.01) between CC volume and thresholds emerged for the MS patients. Conclusion: Measuring treatment benefits of neuroprotective and repair therapies is a well recognized challenge in MS research. The overall findings of this study suggest that these measurements, which involve the transfer of information interhemispherically via the CC, may be promising outcome measures that warrant further scientific exploration to develop a model to measure recovery.
Association between vitamin D status and age-related macular degeneration by genetic risk.

IMPORTANCE Deficient 25-hydroxyvitamin D (25[OH]D) concentrations have been associated with increased odds of age-related macular degeneration (AMD). OBJECTIVE To examine whether this association is modified by genetic risk for AMD and whether there is an association between AMD and single-nucleotide polymorphisms of genes involved in vitamin D transport, metabolism, and genomic function. DESIGN, SETTING, AND PARTICIPANTS Postmenopausal women (N = 913) who were participants of the Carotenoids in Age-Related Eye Disease Study (CAREDS) (aged 54 to <75 years) with available serum 25(OH)D concentrations (assessed October 1, 1993, to December 31, 1998), genetic data, and measures of AMD (n = 142) assessed at CAREDS baseline from May 14, 2001, through January 31, 2004, were studied. MAIN OUTCOMES AND MEASURES Prevalent early or late AMD was determined from graded, stereoscopic fundus photographs. Logistic regression was used to estimate odds ratios (ORs) and 95% CIs for AMD by the joint effects of 25(OH)D (<12, ≥12 to <20, ≥20 to <30, and ≥30 ng/mL) and risk genotype (noncarrier, 1 risk allele, or 2 risk alleles). The referent group was noncarriers with adequate vitamin D status (≥30 ng/mL). Joint effect ORs were adjusted for age, smoking, iris pigmentation, self-reported cardiovascular disease, self-reported diabetes status, and hormone use. Additive and multiplicative interactions were assessed using the synergy index (SI) and an interaction term, respectively. To examine the association between AMD and variants in vitamin D-related genes, age-adjusted ORs and 95% CIs were estimated using logistic regression. RESULTS Among the 913 women, 550 had adequate levels of vitamin D (≥20 ng/mL), 275 had inadequate levels (≥12 to <20 mg/mL), and 88 had deficient levels (<12 ng/mL). A 6.7-fold increased odds of AMD (95% CI, 1.6-28.2) was observed among women with deficient vitamin D status (25[OH]D <12 ng/mL) and 2 risk alleles for CFH Y402H (SI for additive interaction, 1.4; 95% CI, 1.1-1.7; P for multiplicative interaction = .25). Significant additive (SI, 1.4; 95% CI, 1.1-1.7) and multiplicative interactions (P = .02) were observed for deficient women with 2 high-risk CFI (rs10033900) alleles (OR, 6.3; 95% CI, 1.6-24.2). The odds of AMD did not differ by genotype of candidate vitamin D genes. CONCLUSIONS AND RELEVANCE In this study, the odds of AMD were highest in those with deficient vitamin D status and 2 risk alleles for the CFH and CFI genotypes, suggesting a synergistic effect between vitamin D status and complement cascade protein function. Limited sample size led to wide CIs. Findings may be due to chance or explained by residual confounding.
The Photoreactions of Recombinant Phytochrome from the Cyanobacterium Synechocystis: A Low-Temperature UV–Vis and FT-IR Spectroscopic Study

Abstract The interconvertible photoreactions of recombinant phytochrome from Synechocystis reconstituted with phycocyanobilin were investigated by light-induced optical and Fourier-transform infrared (FT-IR) difference spectroscopy at low temperatures for the first time. The photochemistry was found to be deferred below −100°C for the tranformation of red-absorbing form of phytochrome (Pr) → far-red–absorbing form of phytochrome (Pfr), and no formation of an intermediate similar to the photoproduct of phytochrome A obtained at −140°C (lumi-R) was observed. Two intermediates could be stabilized below −40°C and between −40 and −20°C, and were denoted as meta-Ra and meta-Rc, respectively. Above −20°C Pfr was obtained. In the reverse reaction two intermediates could be stabilized below −60°C (lumi-F) and between −60 and −40°C (meta-F). The FT-IR difference spectra of the late Pr → Pfr photoreaction show great similarities to the spectra obtained from oat phytochrome A suggesting similar conformation of the chromophore and interactions with its protein environment, whereas deviations in the spectra of meta-Ra were observed. A large band around 1700 cm−1 in the difference spectra between the intermediates and Pr which is tentatively assigned to the C19=O group of the prosthetic group indicates the Z,E isomerization around the C15=C16-methine bridge of the chromophore during the formation of meta-Ra. In the difference spectra of the parent states only small differences are observed in this region suggesting that the frequency of the carbonyl group is similar in Pr and Pfr. Since the FT-IR difference spectra between lumi-F and Pfr show great similarities to the spectra of the parent states, it is assumed that during the formation of lumi-F the chromophore largely returns into the primary Pr conformation. The FT-IR spectra recorded in a medium of 2H2O generally show a downshift of the significant bands due to the isotope effect. The appearance of a characteristic band around 935 cm−1 in all 2H2O spectra suggests an assignment to an N–2H bending vibration of the chromophore.
Betaine aldehyde dehydrogenase kinetics partially account for oyster population differences in glycine betaine synthesis.

Betaine aldehyde dehydrogenase (BADH), the terminal enzyme of the glycine betaine synthetic pathway was purified 245-fold from the mitochondria of Atlantic and Chesapeake Bay oyster populations acclimated to 350 mosm, using ammonium sulfate precipitation, anion exchange, and affinity chromatography. BADH from both populations functions at its maximum rate at 50-55 degrees C over a broad pH range (7.5-9). BADH activity is also modulated by increased [Na(+)] and [K(+)]. Although BADH from both populations has a similar V(max), BADH from Bay oysters has a substantially lower affinity for its substrate, betaine aldehyde, (K(m) = 0.36 mM), than BADH from Atlantic oysters (K(m) = 0.1 mM). Despite kinetic differences, BADH from both Atlantic and Chesapeake Bay oysters have the same molecular weight based on electrophoretic analysis. These differences in BADH enzyme kinetics between the two oyster populations probably partially explain the lower glycine betaine synthesis rates and concentrations in Chesapeake Bay oysters. J. Exp. Zool. 286:238-249, 2000.
Convergence Aspect of Capital Formation: A Study on Major Countries

Empirical evidences on convergence or divergence of a group of economies or regions in most instances are based upon per capita income as the only determinant for discussion. As time goes on, there has been a lot of studies on the convergence or divergence of certain variables which are proxy to the income variable. The present chapter attempts to examine whether there is convergence or divergence in per capita gross capital formation across 37 countries for the period 1980-2013. The study observes that there is significant absolute β and σ convergence for the cross section of all the economies for the entire period. By segregating the entire data into the categories of developed and developing country, the study further observes significant σ convergence in both the cases with no absolute β convergence in either of the country categories.
Left ventricular hypertrophy independent of hypertension in patients with obstructive sleep apnoea.

To evaluate cardiac structure and function as well as blood pressure in the obstructive sleep apnoea syndrome (OSAS), we investigated 61 male patients and 61 male controls with M-mode and two-dimensional echocardiography. All patients had a history of habitual snoring and a diagnosed light to severe OSAS by previous investigations of nocturnal oxygen saturation status. No subject in the control group had a history of OSAS or hypertension. Body weight was higher in the OSAS patients than in the controls (P less than 0.001). Fifty per cent (31 out of 61) of the OSAS patients had systemic hypertension; 17 of these 31 were on pharmacological antihypertensive treatment. Neither the systolic nor the diastolic blood pressures were found to correlate to the severity of the OSAS (desaturation index). The heart rate was higher at rest in the OSAS patients with or without systemic hypertension compared to the controls with or without a blood pressure level above 165/95 mmHg (P less than 0.05 and P less than 0.01, respectively). Left ventricular (LV) internal dimensions as assessed by echocardiography did not differ between the two groups, while the interventricular septum and the LV posterior wall were thicker in the OSAS group. Thus, the LV mass and the LV mass index were significantly higher among the OSAS patients (P less than 0.001 and P less than 0.001). The LV mass index was approximately 15% higher among the 30 normotensive OSAS patients with no history of cardiac disease compared with the normotensive controls (P less than 0.05). (ABSTRACT TRUNCATED AT 250 WORDS)
Spinal cord injury induction of lesional expression of profibrotic and angiogenic connective tissue growth factor confined to reactive astrocytes, invading fibroblasts and endothelial cells.

OBJECT The glial scar composed of astrogliosis and extracellular matrix deposition represents a major impediment to axonal regeneration. The authors investigated the role of a novel profibrotic and angiogenic peptide connective tissue growth factor (CTGF [Hcs24/IGFBP-r2P]) in glial scar formation following spinal cord injury (SCI) in rats. METHODS The effects of SCI on CTGF expression during glial scar maturation 1 day to 1 month post-SCI were investigated using fluorescein-activated cell sorter (FACS) immunohistochemical analysis; these findings were compared with those obtained in sham-operated (control) spinal cords. The CTGF-positive cells accumulated at the spinal cord lesion site (p < 0.0001) corresponding to areas of glial scar formation. In the perilesional rim, CTGF expression was confined to invading vimentin-positive, glial fibrillary acidic protein (GFAP)-negative fibroblastoid cells, endothelial and smooth-muscle cells of laminin-positive vessels, and GFAP-positive reactive astrocytes. The CTGF-positive astrocytes coexpressed the activation-associated intermediate filaments nestin, vimentin (> 80%), and mesenchymal scar component fibronectin (50%). CONCLUSIONS The restricted accumulation of CTGF-reactive astrocytes and CTGF-positive fibroblastoid cells lining the laminin-positive basal neolamina suggests participation of these cells in scar formation. In addition, perilesional upregulation of endothelial and smooth-muscle CTGF expression points to a role in blood-brain barrier function modulating edema-induced secondary damage.
Upregulation of T-cell Immunoglobulin and Mucin-Domain Containing-3 (Tim-3) in Monocytes/Macrophages Associates with Gastric Cancer Progression

ABSTRACT T-cell immunoglobulin and mucin-domain containing-3 (Tim-3) is an important immune regulatory molecule in cancer immune system. However, expression and function of Tim-3 in monocytes/macrophages in cancer progression mainly remain unclear. In this study, we analyzed Tim-3 levels in peripheral blood mononuclear cells (PBMCs) from 62 gastric cancer patients and 45 healthy controls using flow cytometry and then associated Tim-3 levels with clinical pathological data from patients. We found Tim-3 level was significantly upregulated in monocytes from gastric cancer patients compared with those from healthy controls, and that upregulated Tim-3 levels associated with depth of tumor invasion and tumor lymph node metastasis and advanced clinical stages of gastric cancer patients. Furthermore, tumor-bearing mouse experiments revealed that Tim-3 level on monocytes/macrophages associated with xenograft formation and growth. In addition, culture of monocytes from healthy controls with gastric cancer cell-conditioned medium upregulated Tim-3 expression, but IL-10, TNF-α, IFN-γ, or GM-CSF treatment or T-bet, Eomes, and T-bet/Eomes double gene knockout did not affect Tim-3 levels in blood monocytes/macrophages from human or mouse, respectively. Gal-9/Tim-3 signal was able to significantly stimulate monocyte to secrete IL-6, IL-8, and IL-10, but not IL-1β, IL-12p70, or TNF-α in presence of LPS. In conclusion, our study demonstrated that Tim-3 expressed by monocyte/macrophages might be an important mechanism in gastric cancer progression.
The role of laser fluence in cell viability, proliferation, and membrane integrity of wounded human skin fibroblasts following helium‐neon laser irradiation

In medicine, lasers have been used predominantly for applications, which are broadly termed low level laser therapy (LLLT), phototherapy or photobiomodulation. This study aimed to establish cellular responses to Helium‐Neon (632.8 nm) laser irradiation using different laser fluences (0.5, 2.5, 5, 10, and 16 J/cm2) with a single exposure on 2 consecutive days on normal and wounded human skin fibroblasts.
The origin of foam cells in atherosclerosis.

Abstract The origin of the foam cells of experimental atherosclerotic lesions in rabbits has been investigated. Light and electron microscopic techniques were used. Lesions were induced by comparatively low elevations of serum cholesterol (up to 550 mg./100 ml.) and maintained in a narrow range (450-550 mg./100 ml.) by dietary manipulation. Two types of foam cell are described. One of these is considered to be a modified smooth muscle cell derived from the cells of the arterial media. The second is a macrophage of reticuloendothelial origin probably a blood monocyte. The smooth muscle foam cell is released into the developing plaque by destruction of the elastic laminae to which these cells are normally attached. Active migration of cells through intact or split laminae was not seen. Following assimilation of these cells into the plaque, modifications occur involving predominantly the cell ergastoplasm. Such modifications are considered to reflect activation of these cells to form collagen and elastic fibres in an attempt to regain their resting cell-fibre relationships and repair the damage to the arterial wall. The macrophage foam cell is an extremely active phagocyte which rapidly achieves large size and then degenerates. The cellular debris from this degeneration forms a considerable portion of the gruel core of older plaques. It is suggested that measures to promote the activities of the smooth muscle cell or to inhibit those of the macrophage could be of considerable importance in encouraging healing of atherosclerotic lesions and restoration of normal function to the damaged arterial wall.
Phase I design for completely or partially ordered treatment schedules

The majority of methods for the design of phase I trials in oncology are based upon a single course of therapy, yet in actual practice, it may be the case that there is more than one treatment schedule for any given dose. Therefore, the probability of observing a dose‐limiting toxicity may depend upon both the total amount of the dose given, as well as the frequency with which it is administered. The objective of the study then becomes to find an acceptable combination of both dose and schedule. Past literature on designing these trials has entailed the assumption that toxicity increases monotonically with both dose and schedule. In this article, we relax this assumption for schedules and present a dose‐schedule finding design that can be generalized to situations in which we know the ordering between all schedules and those in which we do not. We present simulation results that compare our method with other suggested dose‐schedule finding methodology. Copyright © 2013 John Wiley & Sons, Ltd.
What Do Americans Talk About When They Talk About Income Inequality?

Rising levels of inequality currently receive a great deal of attention from the mass public. But what do ordinary people have in mind when they talk about inequality? In this study, we use both survey and survey-experimental data to investigate whether Americans understand this highly abstract concept the way that academics have in mind. Results show substantial evidence of misunderstanding, and this helps to explain the relatively weak link between concern about inequality and support for redistributive economic policies.