Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperature dependence of two parameters in a photosynthesis model

The temperature dependence of the photosynthetic parameters Vcmax, the maximum catalytic rate of the enzyme Rubisco, and Jmax, the maximum electron transport rate, were examined using published datasets. An Arrehenius equation, modified to account for decreases in each parameter at high temperatures, satisfactorily described the temperature response for both parameters. There was remarkable conformity in Vcmax and Jmax between all plants at Tleaf 30 °C. For both normalized Vcmax and Jmax, the maximum fractional error introduced by assuming a common temperature response function is 30 °C. The ratio Jmax/Vcmax varies with temperature, but analysis of the ratio at Tleaf = 25 °C using the fitted mean temperature response functions results in Jmax0/Vcmax0 = 2·00 ± 0·60 (SD, n = 43).
Precision Mapping of O-Linked N-Acetylglucosamine Sites in Proteins using Ultraviolet Photodissociation Mass Spectrometry.

Despite its central importance as a regulator of cellular physiology, the identification and precise mapping of O-linked N-acetylglucosamine (O-GlcNAc) post-translational modification (PTM) sites in proteins by mass spectrometry (MS) remains a considerable technical challenge. This is due in part to cleavage of the glycosidic bond occurring prior to the peptide back-bone during collisionally activated dissociation (CAD), which leads to generation of characteristic oxocarbenium ions and impairs glycosite localization. Herein, we leverage CAD-induced oxocarbenium ion generation to trigger ultraviolet photodissociation (UVPD), an alternate high energy deposition method that offers extensive fragmentation of peptides while leaving the glycosite intact. Upon activation using UV laser pulses, efficient photodissociation of glycopeptides is achieved with pro-duction of multiple sequence ions that enable robust and precise localization of O-GlcNAc sites. Application of this method to tryptic peptides originating from O-GlcNAcylated proteins TAB1 and Polyhomeotic confirmed previously reported O-GlcNAc sites in TAB1 (S395 and S396) and uncovered new sites within both proteins. We expect this strategy will complement existing MS/MS methods and be broadly useful for mapping O-GlcNAcylated residues of both proteins and proteomes.
ContribuciÓn a la filogenia del género Paspalum (Poaceae: Panicoideae: Paniceae)

Paspalum L. has approximately 330 species and a large geographical distribution, mainly in tropical and subtropical regions of America. Due to the morphological variability among the species, different authors have proposed dividing the genus into subgenera, sections, or informal groups. A cladistic analysis of Paspalum was conducted using anatomical foliar and exomorphological characters to test its monophyly and its phylogenetic relationships among representative species. The degree of character homoplasy was analyzed in order to estimate the diagnostic value of anatomical characters among groups. For the cladistic analysis, 47 species of 27 groups established by Chase, with modification established by Cialdella et al. and Morrone et al., and 36 exomorphological and anatomical foliar characters were considered. The data matrix was analyzed with Nona and Pee-Wee, parsimony programs using equal weights and implied weighting. The present phylogenetic analysis confirms that Paspalum is a paraphyletic group and shows close relationships with Axonopus and Thrasya in Paniceae.
Risks associated with tandem release of large and small ladybirds (Coleoptera: Coccinellidae) in heterospecific aphidophagous guilds

Abstract Multiple interactions occurring within aphidophagous guilds determine their final predation outcomes, i.e., antagonistic, additive, or synergistic. Based on these predatory outcomes, the suitability of guilds in suppressing aphid pests is determined. The present study assesses the efficacy of 11 guilds, formed from both larval and adult stages of four locally abundant aphidophagous coccinellids (Coleoptera: Coccinellidae), while exploiting the pea aphid, Acyrthosiphon pisum Harris (Hemiptera: Aphididae). The observed antagonistic effects within these guilds are resultants of enhanced predator–predator interactions due to the size and diversity of guild predators. Smaller ladybird predators maintained their usual body mass, probably by increasing their conversion efficiencies to compensate for their reduced prey consumption. However, larger ladybirds reported loss in their body mass, owing to their higher energy needs. The overall guild conversion efficiencies and growth rates were reduced. Among the experimental guilds, the observed prey mortalities were relatively higher in two-predator guilds, and within these two-predator combinations, the higher prey mortalities were recorded in those guilds where Coccinella septempunctata was one of the predators. Résumé Les interactions multiples qui se produisent au sein des guildes d'aphidophages déterminent les résultats finaux de la prédation, par ex. antagonistes, additifs ou synergiques. Nous déterminons l'aptitude des guildes à éliminer les pucerons ravageurs d'après ces résultats de la prédation. Notre étude évalue l'efficacité de 11 guildes formées à la fois de stades larvaires et adultes de quatre coccinellidés (Coleoptera: Coccinellidae) aphidophages localement abondants qui exploitent le puceron du pois, Acyrthosiphon pisum Harris (Hemiptera: Aphididae). Les effets antagonistes observés au sein de ces guildes résultent d'interactions plus importantes entre prédateurs reliées à la taille et la diversité des guildes de prédateurs. Les coccinelles prédatrices de plus petite taille maintiennent leur masse corporelle habituelle, probablement en augmentant leurs rendements de conversion afin de compenser leur consommation réduite de proies. Cependant, les coccinelles plus grandes affichent une perte de masse corporelle à cause de leurs besoins énergétiques accrus. Les rendements de conversion globaux et les taux de croissance des guildes sont réduits. Parmi les guildes expérimentales, les mortalités observées chez les proies sont relativement plus élevées dans les guildes à deux prédateurs, et parmi ces guildes à deux prédateurs, les mortalités de proies plus élevées s'observent dans les guildes dont l'un des prédateurs est Coccinella septempunctata.
Caractéristiques symbiotiques et génotypiques des Rhizobia associés à Acacia saligna (Labili.) Wendl. dans quelques pépinières en Algérie

Abstract This study on the nodulation and symbiotic nitrogen fixation by Acacia saligna in nine nurseries from North and South areas of Algeria indicates that Acacia saligna is mostly nodulated and fix nitrogen. Therefore, nodulation and nitrogen fixation potential were clearly superior for plants from northern nurseries than those from southern ones. Symbiotic and genotypic characteristics of the associated strains indicate that Acacia saligna is nodulated by strains of the genus Bradyrhizobium in northern nurseries and by strains of the genera Sinorhizobium and Rhizobium in the southern ones.
SPOP Deregulation Improves the Radiation Response of Prostate Cancer Models by Impairing DNA Damage Repair

Speckle-type POZ (pox virus and zinc finger protein) protein (SPOP) is the most commonly mutated gene in prostate cancer (PCa). Recent evidence reports a role of SPOP in DNA damage response (DDR), indicating a possible impact of SPOP deregulation on PCa radiosensitivity. This study aimed to define the role of SPOP deregulation (by gene mutation or knockdown) as a radiosensitizing factor in PCa preclinical models. To express WT or mutant (Y87N, K129E and F133V) SPOP, DU145 and PC-3 cells were transfected with pMCV6 vectors. Sensitivity profiles were assessed using clonogenic assay and immunofluorescent staining of γH2AX and RAD51 foci. SCID xenografts were treated with 5 Gy single dose irradiation using an image-guided small animal irradiator. siRNA and miRNA mimics were used to silence SPOP or express the SPOP negative regulator miR-145, respectively. SPOP deregulation, by either gene mutation or knockdown, consistently enhanced the radiation response of PCa models by impairing DDR, as indicated by transcriptome analysis and functionally confirmed by decreased RAD51 foci. SPOP silencing also resulted in a significant downregulation of RAD51 and CHK1 expression, consistent with the impairment of homologous recombination. Our results indicate that SPOP deregulation plays a radiosensitizing role in PCa by impairing DDR via downregulation of RAD51 and CHK1.
Low temperature emergence potential of short season corn hybrids grown under controlled environment and plot conditions

One important reason for limited progress in selecting corn (Zea mays L.) with superior cold tolerance during germination and early growth is the unpredictable occurrence of cold, wet test springs. Breeders need an efficient laboratory test paralleling field emergence under such climatic conditions. Laboratory screening data from 30 corn hybrids with under 2400 corn heat unit ratings were compared to field emergence data in Atlantic Canada to evaluate the usefulness of a laboratory test as an indicator of cold tolerance. Hybrids were ranked by mean percent emergence using 1985–1989 field data collected from seven locations in the Atlantic region. From daily observations on seed germinated in a germinator at 11 °C, mean times to 50% root and coleoptile initiation, and 1-cm coleoptile were calculated using probit analyses. Field emergence ranked from 1 (highest percent) to 30 was compared to ranking of time to 50% 1-cm coleoptile in the laboratory (one represented most rapid growth). Of the top 15 hybrids (.
Molecular data on two mitochondrial genes of a newly discovered crustacean species (Lightiella magdalenina, Cephalocarida)

Cephalocarida is a rare and poorly known class of small benthic crustaceans, consisting of only eleven species belonging to five genera. Thus far, only one species (Hutchinsoniella macracantha) has been studied at molecular level. We report the partial sequences of two phylogenetically important mitochondrial genes (Cytochrome c Oxidase I and Cytochrome b) from the newly discovered Mediterranean species, Lightiella magdalenina. The genetic relationships between the two cephalocarid species are discussed.
Risks for cold frequency vary by sex: role of asthma, age, TLR7 and leukocyte subsets

Viral respiratory infections are usually benign but can trigger asthma exacerbations. The factors associated with upper respiratory tract infection (cold) frequency are not fully understood, nor is it clear whether such factors differ between women and men. To determine which immunological and clinical variables associate with the frequency of self-reported respiratory infections (colds), 150 asthma cases and 151 controls were recruited. Associations between antiviral immune response variables: toll-like receptor (TLR)7/8 gene expression, plasmacytoid dendritic cell (pDC) numbers and interferon-α, tumour necrosis factor and interleukin-12 production, and asthma were then examined that might explain cold frequency. People with asthma cases reported more colds per year (median 3 versus 2; p<0.001) and had lower baseline TLR7 gene expression (odds ratio 0.12; p=0.02) than controls. Associations between many variables and cold frequency differed between women and men. In women, high blood neutrophil counts (β=0.096, p=0.002), and younger age (β=−0.017, p<0.001), but not exposure to children, were independently associated with more frequent colds. In men, low TLR7 expression (β=−0.96, p=0.041) and high CLEC4C gene expression (a marker of pDC; β=0.88, p=0.008) were independently associated with more frequent colds. Poor asthma symptom control was independently associated with reduced TLR8 gene expression (β=−1.4, p=0.036) and high body mass index (β=0.041, p=0.004). Asthma, age and markers of inflammation and antiviral immunity in peripheral blood are associated with frequent colds. Interestingly, the variables associated with cold frequency differed between women and men. Asthma, age and blood markers of antiviral immunity associate with cold frequency in a sex-dependent manner. People with asthma have lower TLR7 gene expression than healthy people; only in men does this associate with cold frequency. https://bit.ly/3e3yWKy
Cracker shape modifies ad libitum snack intake of crackers with cheese dip

Abstract Food and energy intake can be effectively lowered by changing food properties, but little is known whether modifying food shape is sufficient to influence intake. This study investigated the influence of cracker shape and cheese viscosity on ad libitum intake of cracker–cheese combinations. Forty-four participants (thirteen males, 23 (sd 3) years, BMI 21 (sd 2) kg/m2) participated in four late afternoon snack sessions (2 × 2 randomised crossover design). Iso-energetic crackers were baked into flat squares and finger-shape cylindrical sticks and combined with a cheese dip varying in viscosity. Approximately eighty crackers and 500 g cheese dip were served in separate large bowls. Participants consumed crackers with cheese dip ad libitum while watching a movie of 30 min. Dipping behaviour and oral processing behaviour were measured simultaneously by hidden balances under the cheese bowls and video recordings. Cracker intake (28 (sem 1) crackers) of cracker–cheese combinations was not influenced by cracker shape. Cheese intake of cracker–cheese combinations was 15 % higher for flat-squared than finger-shape crackers (131 kJ, P = 0·016), as a larger amount of cheese was scooped with flat-squared crackers (2·9 (sem 0·2) v. 2·3 (sem 0·1) g cheese per dip, P < 0·001) and showed higher eating rate and energy intake rate (P < 0·001). Eating rate over snacking time decreased by reducing bite frequency (P < 0·001) while cheese dip size remained fairly constant (P = 0·12). Larger energy intake from condiments was facilitated by increased cracker surface, and this did not trigger earlier satiation. Changing food carrier surface may be a promising approach to moderate energy intake of often high energy dense condiments, sauces and toppings.
Long‐term benefit of enzyme replacement therapy with alglucosidase alfa in adults with Pompe disease: Prospective analysis from the French Pompe Registry

Despite a wide clinical spectrum, the adult form of Pompe disease is the most common one, and represents more than 90% of diagnosed patients in France. Since the marketing of enzyme replacement therapy (alglucosidase alfa, Myozyme), all reports to date in adults demonstrated an improvement of the walking distance, and a trend toward stabilization of respiratory function, but the majority of these studies were less than 5 years of duration. We report here the findings from 158 treated patients included in the French Pompe Registry, who underwent regular clinical assessments based on commonly used standardized tests (6‐minute walking test, MFM scale, sitting vital capacity, MIP and MEP). For longitudinal analyses, the linear mixed effects models were used to assess trends in primary endpoints over time under ERT. A two‐phase model better described the changes in distance traveled in the 6‐minute walk test and MFM. 6MWT showed an initial significant increase (1.4% ± 0.5/year) followed by a progressive decline (−2.3%/year), with a cut‐off point at 2.2 years. A similar pattern was observed in total MFM score (6.6% ± 2.3/year followed by a − 1.1%/year decline after 0.5 years). A single‐phase decline with a slope of −0.9 ± 0.1%/year (P < .001) was observed for FVC, and MEP remained stable over the all duration of follow‐up. This study provides further evidence that ERT improves walking abilities and likely stabilizes respiratory function in adult patients with Pompe disease, with a ceiling effect for the 6MWT in the first 3 years of treatment.
From NIMBYsm to the 15M: A Decade of Urban Conflicts in Barcelona and Valencia

Abstract The first decade of the 21st century was a period of economic and demographic expansion and impressive urban development in Spain's big cities, including Barcelona and Valencia. This growth came along with a great effort to develop new territorial, sectoral and urban plans which would direct it, but which were not always successful. Nevertheless, these planning endeavors were not without critiques from social agents. In fact, throughout that decade we observed a growing distrust towards the institutional forms of citizen representation, and the ways and procedures of urban governance and spatial planning. This paper shows some important results of a systematic analysis based on print-media of urban conflicts related to land-use changes that emerged during a critical time period in two Spanish metropolitan areas: Barcelona and Valencia. The aim of this paper is to compare the evolution of urban conflicts in both cities that occurred between 2002 and 2012, from the point of view of social movements and their activists. The analysis of conflict activity between both cities gives interesting clues about where and why conflicts emerge and adds some pertinent reflections on the increasing problems of metropolitan governance in Spanish cities. During the mentioned period a deep transformation was witnessed in the types of conflicts that tend to emerge in these cities: from the reactive and isolated not in my back yard-like campaigns to broader protest movements like the 15 movement in the 2010s. The new movements appear to be participating actively in land-use or locational conflicts, but in fact reach far beyond these specific plans. They criticize not only the specific plans, but use this criticism to launch broader critiques of how their city is ruled and for whom.
Comparison of albumin dialysis devices molecular adsorbent recirculating system and ADVanced Organ Support system in critically ill patients with liver failure—A retrospective analysis

Extracorporeal albumin dialysis (ECAD) represents a supplemental therapy for patients with liver failure. Most experience was gained with the molecular adsorbent recirculating system (MARS). However, the ADVanced Organ Support (ADVOS) system was recently introduced. This study aims to compare effects of MARS and ADVOS on biochemical and clinical parameters in critically ill patients with liver failure using a retrospective analysis of ECAD at Jena University Hospital. Laboratory parameters, health scoring values, and need for transfusion were recorded before and after treatment. Generalized estimating equations were used to account for repeated measurements of multiple ECAD cycles per patient. Between 2012 and 2017, n = 75 MARS and n = 58 ADVOS cycles were evaluated. Although ADVOS runs significantly longer, both devices provided comparable reduction rates of bilirubin (MARS: −48 [−80.5 to −18.5] μmol/L vs ADVOS: −35 [−87.8 to −2.0] μmol/L, P = .194), a surrogate for detoxification capacity, while urea and lactate levels were more significantly lowered by the ADVOS system. In cycles with similar treatment times, both systems provided comparable reduction rates for bilirubin, renal replacement, coagulation, and metabolic parameters. Citrate was the preferred anticoagulant in case of bleeding. Neither bleeding tendency nor fibrinogen levels or platelets were altered by the type of anticoagulation. No adverse events were reported, but two sessions (one MARS and one ADVOS) were terminated early due to filter clotting. Experience is needed in the application of ADVOS and more prospective trials comparing the detoxification capacity of ECAD devices are needed to support and enlarge the findings of the current evaluation.
The importance of smaller veteran trees

The inexorable growth of towns and cities places great strain and pressure on urban tree populations – the “urban forest”. Arguably, it is in the urban catchment that trees delivered the greatest benefits and “services” to local people, but also are under the greatest stresses. Urban or urbanised environments exhibit many characteristics that make life difficult and problematic for big trees, and yet it is the larger trees that bring the greatest contributions to quality of life, to landscapes, to human health, to floodwater mitigation, to climate-change adaptation, to house values and the desire to live in a particular locale, to biodiversity, and to heritage or “sense of place”. Furthermore, with urban environmental pressures and stresses, ecosystems flux and change under a burden of climate-change, of nutrient fallout, of new invasive species (including diseases and pests), and both human-induced disturbance on the one hand, and the ending of long-term management on the other. This situation provides a background context to a selection of research papers on urban trees, urban forests and urban landscapes.
Subunit Structure of Phenoloxidase Purified from the Larvae of Housefly

The subunit structure of phenoloxidase from the larvae of housefly, Musca domestica vicina Maquart, was investigated by urea treatment, SDS-polyacrylamide gel electrophoresis and electron microscopy. Phenoloxidase was dissociated into a single type of subunit (MW 6.5 × 104) by 5 m urea treatment. A similar subunit (MW 6.1 × 104) was also detected by SDS-polyacrylamide gel electrophoresis. Furthermore, four additional protein bands with molecular weights of 4.8 × 104, 3.5 × 104, 2.4 × 104 and 1.2 × 104 were detected by SDS-polyacrylamide gel electrophoresis by extensive incubation of phenoloxidase with SDS. A cylindrical molecular structure was deduced from the electron microscopic analysis. The outside and inside diameter and the height of phenoloxidase molecule were evaluated to be 100, 50 and 70 A, respectively.
Application of Quantitative Real-Time Polymerase Chain Reaction for Noninvasive Genetic Monitoring

Abstract Noninvasive genetic monitoring of animal populations has become a widely used method in animal conservation and wildlife management due to its known advantages in sample availability of endangered or elusive species. A variety of methods have been suggested to overcome the difficulties of collecting reliable genetic data despite poor DNA quality and quantity of samples. We used quantitative real-time polymerase chain reaction (qPCR) to quantify DNA contents and preselect extracts suitable for microsatellite genotyping of noninvasive samples from 2 carnivore species, wolf (Canis lupus) and Eurasian otter (Lutra lutra). We tested 2 concentration thresholds for DNA extracts containing either 5 pg/µL or 25 pg/µL at minimum and evaluated the effect of excluding samples from genotyping falling below either of these DNA concentrations. Depending on species and threshold concentration applied, we reduced the genotyping effort by 21% to 47% and genotyping errors by 7% to 45%, yet we could still detect 82% to 99% of available genotypes. Thus, qPCR may potentially reduce genotyping effort and enhance data reliability in noninvasive genetic studies. Genetic laboratories working on noninvasive population genetic studies could transfer this approach to other species, streamline genetic analyses and, thus, more efficiently provide wildlife managers with reliable genetic data of wild populations.