Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrating fire risk into forest planning

The present thesis deals with the inclusion of fire risk considerations into forest planning in Catalonia (North-East Spain). The first part of the thesis focused on the modeling the susceptibility of different kinds of forest to fire (Studies I, II, III and IV), and the second part on the inclusion of the acquired knowledge about fire risk into forest planning systems (Studies V and VI). The models were developed for forest planning purposes, all the predictors being easily obtainable through forest inventories or forest simulators, some of them being also dependent on forest management. Studies I and II developed models for predicting the probability of fire occurrence, using data on fire perimeters, the Spanish forest map (MFE50), and the second Spanish Forest Inventory. In Study III, models to predict the fire damage at stand level and the post-fire tree survival probability were developed using data from fire perimeters and from the second and third Spanish Forest Inventory. The models developed in Study IV were based on the opinions of experts with respect to the vulnerability of different forest stands to fire. Studies I and II showed that elevation plays a mayor role in determining the probability of fire occurrence, forest stands located in lower elevations being more frequently affected by fires. The results obtained also indicate that mature stands, with low vertical irregularity, and no presence of ground vegetation have the lowest risk of fire. Large trees in dominant positions are the least susceptible to fire mortality. The model developed in Study II for predicting the probability of fire occurrence was included in two different planning applications. The first application (Study V), solved a stand level problem on the optimal management when the objective function was maximized subject to fire risk. The second application (Study VI) consisted of a landscape level problem where different landscape metrics were analysed as means to modify the spatial configuration of a forest landscape through forest planning, taking into account the stands’ fire resistance. The summary of the thesis also presents a regional scenario analysis in which the developed models to predict the probability of fire occurrence, degree of damage, and probability of tree survival were used in simulations, which predict the standing and harvested volume of timber. The studies indicate that the optimal rotations of stands shorten when the risk of fire increases. The timber yields at a regional level can be significantly overestimated (10-20%) if the risk of fire is not considered.
Reconfigurable Supercomputing with Scalable Systolic Arrays and InStream Control for Wavefront Genomics Processing

Computational challenges in genomics data mining and analysis are an impending roadblock in modern health-sciences research, where algorithms for DNA sequence processing grow alarmingly in computational needs as datasets from new instruments continue to dramatically expand. Reconfigurable computers featuring customizable processing devices (e.g. FPGAs) hold the key in addressing these challenges with high performance, productivity, and sustainability, where the architecture adapts to match the unique needs of each application instead of vice-versa. In this paper, we present the novel use of a method for incorporating control information into the data stream, limiting wasted cycles and increasing hardware utilization. This method is described in Section II, and then featured in Section III as device-level reconfigurable architectures for in-stream control with scalable systolic arrays to accelerate two leading genomics applications based upon wavefront algorithms, NeedlemanWunsch (NW) and Smith-Waterman (SW) [1], and a third application, Needle-Distance (ND) [2], an augmentation of NW. These architectures are experimentally evaluated on Novo-G, the reconfigurable supercomputer in the NSF CHREC Center at Florida, where results achieve unprecedented levels of sustained performance for these problems. Case-study results are reported in Section IV, followed by Section V with summary and conclusions.
Layer-specific manganese-enhanced MRI of the retina in light and dark adaptation.

PURPOSE To employ functional manganese-enhanced MRI (MEMRI) to image layer-specific changes in calcium-dependent activities in the rat retina during light versus dark adaptation. METHODS Functional MEMRI at 20 × 20 × 700 μm was used to study light and dark adaptation in the same animals (N = 10) in which one eye was covered and the fellow eye was not. The activity encoding of the light and dark adaptation was achieved in awake conditions and imaged under anesthesia. T(1)-weighted MRI at 11.7 tesla (T) was performed using two identical radiofrequency transceiver coils to allow interleaved MRI acquisitions of the two eyes. An intravascular contrast agent was also used to verify layer assignments. RESULTS MEMRI detected contrasts among the inner retina, outer retina, and choroid. Independent confirmation of the vascular layers and boundaries between layers was documented with an intravascular contrast agent. The retinal layer thicknesses agreed with published data. The outer retina had lower MEMRI activity in light compared with dark adaption (P < 0.001), consistent with the increased metabolic demand associated with the "dark current. " The inner retina had higher MEMRI activity in light compared with dark adaption (P < 0.05). The choroid MEMRI activity was not statistically different between light and dark adaptation (P > 0.05). CONCLUSIONS This study demonstrated a high-resolution MEMRI protocol to image functional activities among different layers of the retinas in awake animals during light and dark adaptation. This approach could have potential applications in animal models of retinal dysfunction.
Revision of failed humeral head resurfacing arthroplasty

Purpose: The purpose of this study is to assess the outcomes of a consecutive series of patients who underwent revision surgery after humeral head resurfacing (HHR). Our joint registry was queried for all patients who underwent revision arthroplasty for failed HHR at our institution from 2005 to 2010. Eleven consecutive patients (average age 54 years; range 38-69 years) that underwent revision of 11 resurfacing arthroplasties were identified. The primary indication for resurfacing had been osteoarthritis in six, glenoid dysplasia in two, a chondral lesion in two, and postinstability arthropathy in one patient. The indication for revision was pain in 10 and infection in one patient. Seven patients had undergone an average of 1.9 surgeries prior to resurfacing (range 1-3). Materials and Methods: All patients were revised to stemmed arthroplasties, including one hemiarthroplasty, two reverse, and eight anatomic total shoulder arthroplasties at a mean 33 months after primary resurfacing (range 10-131 months). A deltopectoral approach was used in seven patients; four patients required an anteromedial approach due to severe scarring. Subscapularis attenuation was found in four cases, two of which required reverse total shoulder arthroplasty. Bone grafting was required in one glenoid and three humeri. Results: At a mean follow-up of 3.5 years (range 1.6-6.9 years), modified Neer score was rated as satisfactory in five patients and unsatisfactory in six. Abduction and external rotation improved from 73° to 88° (P = 0.32) and from 23° to 32° (P = 0.28) respectively. Reoperation was required in two patients, including one hematoma and one revision for instability. Conclusion: Outcomes of revision of HHR arthroplasty in this cohort did not improve upon those reported for revision of stemmed humeral implants. A comparative study would be required to allow for definitive conclusions to be made.
Assessing remission in clinical practice.

OBJECTIVE Remission constitutes the best achievable state in patients with rheumatoid arthritis. We aimed at evaluating sustained remission in a large cohort of patients followed prospectively in clinical practice and to evaluate available instruments to define remission for their stringency in defining this state. PATIENTS AND METHODS We analysed remission and sustained remission in 621 patients who had two consecutive and complete clinical observations; the average period between the two visits was 92 days (median; quartiles: 82; 105). Remission was evaluated according to modified ACR (mACR), 28 Joint Disease Activity Score (DAS28), Simplified Disease Activity Index (SDAI) and Clinical Disease Activity Index (CDAI) criteria. Sustained remission was defined as remission at both consecutive visits. Patients were treated with traditional disease- modifying antirheumatic drugs, mainly methotrexate, and partly with biological agents (approximately 11%). RESULTS Remissions at any one of the two visits were seen in 33.5% of patients by SDAI or CDAI, 42.7% by DAS28, and 38.6% by mACR criteria (P < 0.01). Sustained remission was observed in much lower proportions of patients (between 16.7 and 19.6%, dependent on the instrument). Agreement between classifications of remission by kappa-statistics was very good for SDAI vs CDAI, good for DAS28 vs SDAI or CDAI, and only moderate for mACR vs the three other scores. Residual swollen joints were observed in 15% of patients in DAS28 remission (range 1-9), 6% of patients in mACR remission (range 1-8), but only approximately 5% of patients in CDAI or SDAI remission (range 1-2) (P < 0.01). CONCLUSION Sustained remission can be observed in 17-20% of patients in clinical practice. CDAI and SDAI remission criteria are more stringent than DAS28 and mACR criteria, since they allow for lesser residual disease activity. Consequently, smaller proportions of patients are classified as in remission by SDAI and CDAI than by DAS28 and mACR criteria. Sustained remission is an achievable goal in clinical practice even with the most stringent of the definitions studied.
Interaction of PIN and PGP transport mechanisms in auxin distribution-dependent development

The signalling molecule auxin controls plant morphogenesis via its activity gradients, which are produced by intercellular auxin transport. Cellular auxin efflux is the rate-limiting step in this process and depends on PIN and phosphoglycoprotein (PGP) auxin transporters. Mutual roles for these proteins in auxin transport are unclear, as is the significance of their interactions for plant development. Here, we have analysed the importance of the functional interaction between PIN- and PGP-dependent auxin transport in development. We show by analysis of inducible overexpression lines that PINs and PGPs define distinct auxin transport mechanisms: both mediate auxin efflux but they play diverse developmental roles. Components of both systems are expressed during embryogenesis, organogenesis and tropisms, and they interact genetically in both synergistic and antagonistic fashions. A concerted action of PIN- and PGP-dependent efflux systems is required for asymmetric auxin distribution during these processes. We propose a model in which PGP-mediated efflux controls auxin levels in auxin channel-forming cells and, thus, auxin availability for PIN-dependent vectorial auxin movement.
Synthesis and application of virus‐based hybrid nanomaterials

A virus is a nanoscaled biomolecular substance composed of genes, protecting capsid proteins, and envelopes. The nanoscale dimensions and surface functionalities of virions have been exploited to attract and assemble inorganic and organic materials to produce functional nanomaterials with large surface areas. Genetic modifications of virus capsid proteins lead to the selective deposition and controlled growth of inorganic substances producing organized virus‐based hybrid materials. Due to these properties, viruses hold promise for development as platforms for the creation of hybrid materials with multiple functionalities. This article reviews the characteristics of commonly used viruses and their fabrication into virus‐based hybrid materials that have been applied in engineering applications such as nanowires and catalysts. Biotechnol. Bioeng. 2012;109: 16–30. © 2011 Wiley Periodicals, Inc.
Mini-Nutritional Assessment predicts functional decline of elderly Taiwanese: result of a population-representative sample

Nutrition is a key element in geriatric health and is important for functional ability. The present study examined the functional status-predictive ability of the Mini-Nutritional Assessment (MNA). We analysed the dataset of the ‘Survey of Health and Living Status of the Elderly in Taiwan’, a population-based study conducted by the Bureau of Health Promotion of Taiwan. Study subjects ( ≥ 65 years old) who completed both the 1999 and 2003 surveys were rated with the long form and short form of the MNA at baseline and with the Activities of Daily Living (ADL) and the Instrument Activities of Daily Living (IADL) scales 4 years later (end-point). The ability of the MNA to predict ADL or IADL dependency was evaluated with logistic regression models. The results showed that the elderly who were rated malnourished or at risk of malnutrition at baseline generally had significantly higher ADL or IADL scores 4 years later. Lower baseline MNA scores also predicted a greater risk of ADL or IADL dependency. These associations exist even among the elderly who were free of ADL or IADL dependency at baseline. The results clearly indicate that the MNA is able to predict ADL and IADL dependency (in addition to rating current nutritional status) of the elderly. The MNA, especially the short form, should be a valuable tool for identifying elderly at risk of functional decline and/or malnutrition in clinical practice or community programmes.
Clues of Personal Events in Online Photo Sharing

There is currently a trend in media management and the semantic web to develop new media processing methods and knowledge representation techniques to organise and structure media around events. While this increased interest for events as the central aggregator when organising media is supported by strong research in the fields of knowledge representation and computer vision; it is not yet clear how the digital era users use events when sharing their personal media collection. In this paper, we explore how users share photos online and discuss the results of a preliminary automatic processing of the data collected. We show that while media sharing services do not support events as yet, users still share their media around personal events, either by providing explicit spatio-temporal metadata, or by using an event-centric vocabulary.
Self‐Pollination by Sliding Pollen in Caulokaempferia coenobialis (Zingiberaceae)

Caulokaempferia coenobialis (Zingiberaceae) forms dense populations on steep cliffs in shady, humid monsoon forests in south China. It produces few consecutively opening bright yellow flowers that are 3 cm long and oriented parallel to the ground. Upon anther dehiscence at about 0600 hours, each pollen sac releases a drop of pollen onto the horizontally oriented style, and the two drops then merge to form an oily film that slowly flows toward the stigma, carrying out self‐pollination between about 1500 and 0730 hours the next day. The distance covered by the pollen film is ca. 3 mm. There is no significant difference in fruit set between experimentally cross‐ and self‐pollinated flowers or between naturally pollinated and bagged flowers. The low pollen/ovule ratio of \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$6\pm 4$$ \end{document} probably relates to the pollen grains being held together by pollen‐connecting threads. The latter ensure that pollen grains always arrive as multiples, and this is the first report of such threads in the Zingiberaceae. During 35 h of observation at several locations and during three flowering periods, only three individual bees, five flies, and two butterflies visited single flowers. It remained unclear whether they affected pollination because no return visits were observed. The automatic selfing by pollen that reaches the stigma ca. 9 h after the onset of anthesis apparently constitutes a case of delayed selfing, providing reproductive reassurance in situations of low pollinator visitation.
Genetically Depauperate in the Continent but Rich in Oceanic Islands: Cistus monspeliensis (Cistaceae) in the Canary Islands

Background Population genetic theory holds that oceanic island populations are expected to have lower levels of genetic variation than their mainland counterparts, due to founder effect after island colonization from the continent. Cistus monspeliensis (Cistaceae) is distributed in both the Canary Islands and the Mediterranean region. Numerous phylogenetic results obtained in the last years allow performing further phylogeographic analyses in Cistus. Methodology/Principal Findings We analyzed sequences from multiple plastid DNA regions in 47 populations of Cistus monspeliensis from the Canary Islands (21 populations) and the Mediterranean basin (26 populations). The time-calibrated phylogeny and phylogeographic analyses yielded the following results: (1) a single, ancestral haplotype is distributed across the Mediterranean, whereas 10 haplotypes in the Canary Islands; (2) four haplotype lineages are present in the Canarian Islands; (3) multiple colonization events across the archipelago are inferred; (4) the earliest split of intraspecific lineages occurred in the Early to Middle Pleistocene (<930,000 years BP). Conclusions/Significance The contrasting pattern of cpDNA variation is best explained by genetic bottlenecks in the Mediterranean during Quaternary glaciations, while the Canarian archipelago acted as a refugium of high levels of genetic diversity. Active colonization across the Canarian islands is supported not only by the distribution of C. monspeliensis in five of the seven islands, but also by our phylogeographic reconstruction in which unrelated haplotypes are present on the same island. Widespread distribution of thermophilous habitats on every island, as those found throughout the Mediterranean, has likely been responsible for the successful colonization of C. monspeliensis, despite the absence of a long-distance dispersal mechanism. This is the first example of a plant species with higher genetic variation among oceanic island populations than among those of the continent.
Region and dynamic specificities of adult neural stem cells and oligodendrocyte precursors in myelin regeneration in the mouse brain

Myelin regeneration can occur in the brain following demyelination. Parenchymal oligodendrocyte progenitors (pOPC) are known to play a crucial role in this process. Neural stem cells (NSC) residing in the ventricular-subventricular zone (V-SVZ) also have the ability to generate oligodendrocytes but their contribution to endogenous myelin repair was so far considered to be negligible. Here, we addressed the relative contribution of pOPC and V-SVZ-derived neural progenitors (SVZdNP) to remyelination in cuprizone mouse models of acute or chronic corpus callosum (CC) demyelination. Using genetic tracing, we uncover an unexpected massive and precocious recruitment of SVZdNP in the anterior CC after acute demyelination. These cells very quickly adopt an oligodendrocytic fate and robustly generate myelinating cells as efficiently as pOPC do. In more posterior areas of the CC, SVZdNP recruitment is less important whereas pOPC contribute more, underlining a regionalization in the mobilization of these two cell populations. Strikingly, in a chronic model when demyelination insult is sustained in time, SVZdNP minimally contribute to myelin repair, a failure associated with a depletion of NSC and a drastic drop of progenitor cell proliferation in V-SVZ. In this context, pOPC remain reactive, and become the main contributors to myelin regeneration. Altogether our results highlight a region and context-dependent contribution of SVZdNP to myelin repair that can equal pOPC. They also raise the question of a possible exhaustion of V-SVZ proliferation potential in chronic pathologies.
P2X7R is involved in the progression of atherosclerosis by promoting NLRP3 inflammasome activation

Purinergic 2X7 receptor (P2X7R) and nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3) are expressed in macrophages in atherosclerotic lesions. However, the mechanisms through which P2X7R participates in the inflammatory response in atherosclerosis remain largely unknown. The aim of the present study was to investigate the role of P2X7R in atherosclerosis and the mechanisms of action of the NLRP3 inflammasome following stimulation with oxidized low-density lipoprotein (oxLDL). We observed the expression and distribution of P2X7R in the atherosclerotic plaque in the coronary arteries from an autopsy specimen and in that of the aortic sinuses of apoE−/− mice by immunohistochemistry and immunofluorescence staining. The specificity of short interfering RNA (siRNA) was used to suppress P2X7R and NLRP3 mRNA expression. RT-qPCR and western blot analysis were used to analyze mRNA and protein expression, respectively. Co-immunoprecipitation was used to examine the interaction between protein kinase R (PKR) phosphorylation and NLRP3. P2X7R and NLRP3 were expressed at high levels in the atherosclerotic plaque in the coronary arteries. Stimulation with oxLDL upregulated P2X7R, NLRP3 and interleukin (IL)-1β expression. P2X7R knockdown by siRNA suppressed NLRP3 inflammasome activation by inhibiting the PKR phosphorylation mediated by oxLDL. In the atherosclerotic lesions in the aortic sinuses of apoE−/− mice, P2X7R expression was found at high levels. Moreover, P2X7R siRNA attenuated the development of atherosclerosis in the apoE−/− mice. In conclusion, our results demonstrate that P2X7R plays a significant role in the development of atherosclerosis and regulates NLRP3 inflammasome activation by promoting PKR phosphorylation.
Efficacy of the ketogenic diet for infantile spasms.

OBJECTIVE The objective of this study was to determine whether the ketogenic diet is safe, well-tolerated, and efficacious in the treatment of infantile spasms. METHODS During a 4-year period, 23 children with infantile spasms, aged 5 months to 2 years, were started on the ketogenic diet; 9 (39%) had symptomatic infantile spasms, and 16 (70%) had hypsarrhythmia. Children had an average prediet exposure to 3.3 anticonvulsants. Two children were enrolled before any medication had been tried. Seizure reduction was analyzed retrospectively, using parent reports and electroencephalograms (EEGs) when available. RESULTS At 3, 6, 9, and 12 months, 38%, 39%, 53%, and 46%, respectively, of all patients currently on the diet were >90% improved (3 were seizure-free at 12 months); 67%, 72%, 93%, and 100% were >50% improved. Fifty-six percent remained on the diet at 12 months, 46% of whom were >90% improved and 100% were >50%. Fifty percent of those with hypsarrhythmia and follow-up EEGs had EEG improvement. Fifty-seven percent had their medications reduced or discontinued by 12 months. Fifty-seven percent had improvement in development, which was correlated with seizure control. Independent factors that predicted improvement included age younger than 1 year and previous exposure to 3 or fewer anticonvulsants. No child has died, and 7 children had diet-related adverse reactions (nephrolithiasis, gastroesophageal reflux). DISCUSSION The ketogenic diet is a safe, well-tolerated, and possibly effective potential alternative to other therapies for infantile spasms.