Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular characterization of the type II secretion system of the phytopathogenic bacterium Dickeya dadantii : structural and functional studies of the interaction of OutC and OutD

The type II secretion system (T2SS) is widely exploited by Gram-negative bacteria to secrete diverse virulence factors from the periplasm into the extra-cellular milieu. The phytopathogenic bacterium Dickeya dadanti (ex. Erwinia chrysanthemi) uses this system, named Out, to secrete several cell-wall degrading enzymes that cause soft-rot disease of many plants. The two core components of the Out system, the inner membrane protein OutC and the secretin OutD, which forms a secretion pore in the outer membrane, are involved in secretion specificity. The interaction between OutC and OutD could assure the structural and functional integrity of the secretion system by connecting the two membranes. To understand structure-function relationships between these two components and characterize their interaction sites, we applied an integrative approach involving in vivo cysteine scanning and disulfide cross-linking analysis, truncation analysis of OutC and OutD combined with in vitro GST pull-down, and structural analysis of these proteins and of their interactions by NMR. Our results indicate the presence of at least three interacting sites between the periplasmic regions of OutC and OutD and suggest a β-strand addition mechanism for these interactions. We demonstrated that one site of the HR domain of OutC can interact with two distinct sites of OutD suggesting an alternative mode of their interactions. The presence of exoproteins or/and the inner membrane components of the system OutE-L-M differently alters the affinity of the three OutC-OutD interacting sites. We suggest that successive interactions between these distinct regions of OutC and OutD may have functional importance in switching the secretion machinery between different functional states. To study the mechanism of the targeting and assembly of the secretin OutD into the outer membrane, we exploited the interactions between OutD and two auxiliary proteins, i.e., the inner membrane protein OutB and the outer membrane lipoprotein OutS. We showed a direct interaction between the periplasmic domain of OutB and the N0 domain of OutD. Structure-function analysis of OutS-OutD complex shows that the pilotin OutS binds tightly to 18 residues close to the C-terminus of the secretin subunit causing this unstructured region to become helical on forming the complex. This work allows us to better understand the assembly and function mechanism of the type II secretion system.
Shading Induced Variability in Azalea Mediates its Suitability as a Host for the Azalea Lace Bug

This study quantified how different shading levels alter the foliar nutrient, C:N ratio, chlorophyll content and key leaf characters in azalea 'Delaware Valley Whiteʼ Rhododendron mucronatum (Blume) (Ericales: Ericaceae), which infl uenced, in turn, feeding, oviposition, survival and development of the azalea lace bug, Stephanitis pyrioides (Scott) (Heteroptera: Tingidae). The mean contents of N, Ca, Fe, and Zn increased linearly with increases in the shading level, whereas P, K, B, Mn, and the C:N ratio of leaves were signifi cantly decreased. Although injured leaves contained signifi cantly less chlorophyll than uninjured leaves, the mean relative chlorophyll content of leaves increased linearly with the level of shading. Mean leaf area and moisture content of leaves increased linearly with increased degree of shading, while the mean trichome density decreased. The mean number of oviposited eggs and the percent of nymphs reaching adulthood increased linearly with the degree of shading. Azalea shoots suffered increased feeding injury as the season progressed, yet unshaded plants suffered more feeding injury than shaded plants. While the mean number of eggs laid, and the mean number of reared adults, were signifi cantly and positively correlated with the mean leaf N, the mean feeding injury was negatively correlated with leaf N. Although these dependent variables were not correlated with K nor Ca, the mean number of eggs laid, and the mean number of reared adults were negatively correlated with the mean leaf P and with the mean C:N ratio. Mean feeding injury was positively correlated with leaf P and with the C:N ratio, but negatively correlated with N. This study shows that shaded plants are of better quality as hosts and that these plants can tolerate infestations by the lace bug.
Songbird and Medium‐Sized Mammal Communities Associated with Exurban Development in Pitkin County, Colorado

Abstract: Residential development is occurring at unprecedented rates in the Rocky Mountain region of the United States, with unknown ecological consequences. We conducted our research in exurban development in Pitkin County, Colorado, between May and June in 1998 and 1999. Unlike suburban development, exurban development occurs beyond incorporated city limits, and the surrounding matrix remains the original ecosystem type. We surveyed songbirds and medium‐sized mammals at 30, 180, and 330 m away from 40 homes into undeveloped land to examine the effect of houses along a distance gradient, and in developments of two different housing densities as well as undeveloped sites to examine the effect of housing density. We placed bird species into one of two groups for the house‐distance effect: (1) human‐adapted species, birds that occurred in higher densities close to developments and lower densities farther away and (2) human‐sensitive species, birds that occurred in highest densities farthest from homes and in lowest densities close to development. For both groups, densities of individual species were statistically different between the 30‐ and 180‐m sites. Six species were classified as human‐adapted, and six were classified as human‐sensitive for the house‐distance effect. Dogs (Canis familiaris) and house cats ( Felis domesticus) were detected more frequently closer to homes than farther away, and red foxes ( Vulpes vulpes) and coyotes (Canis latrans) were detected more frequently farther away from houses. With respect to the effect of housing density, most avian densities did not differ significantly between high‐ and low‐density development but were statistically different from undeveloped sites. Six species were present in higher densities in developed areas, and eight species were present in higher densities in undeveloped parcels. Similar results were found for mammalian species, with dogs and cats detected more frequently in high‐density developments and red foxes and coyotes detected more frequently in undeveloped parcels of land. From an ecological standpoint, it is preferable to cluster houses and leave the undeveloped areas in open space, as opposed to dispersing houses across the entire landscape.
A computer‐operated routine of gas exchange and optical measurements to diagnose photosynthetic apparatus in leaves

Photosynthesis is a complex process whose rate is affected by many biochemical and biophysical factors. Fortunately, it is possible to determine, or at least estimate, many of the most important parameters using a combination of optical methods and gas transient analyses. We describe here a computer-operated routine that has been developed to make detailed assessments of photosynthesis at a comprehensive level. The routine comprised the following measurements: steady-state light and CO 2 response curves of net CO 2 assimilation at 21 and 2 kPa O 2 ; transients from limiting to different saturating CO 2 concentrations at 2 kPa O 2 ; post-illumination CO 2 fixation transient; dark‐light induction of O 2 evolution; O 2 yield from one saturating single-turnover flash; chlorophyll fluorescence F 0 , F s and F m during the light and CO 2 response curves; leaf transmission at 820 nm (P700 + ) during the light and CO 2 response curves; post-illumination re-reduction time of P700 + . The routine was executed on a two-channel fast-response gas exchange measurement system (A. Laisk and V. Oja: Dynamic Gas Exchange of Leaf Photosynthesis. CSIRO, Canberra, Australia). Thirty-six intrinsic characteristics of the photosynthetic machinery were derived, including quantum yield of CO 2 fixation ( Y CO2 ), time constant of P700 re-reduction ( τ ′′′ ′ ), relative optical cross-sections of PSII and PSI antennae ( a II , a I ), PSII and PSI density per leaf area unit, plastoquinone pool, total mesophyll resistance, mesophyll diffusion resistance, V m , K m (CO 2 ) and CO 2 /O 2 specificity of Rubisco, RuBP pool at CO 2 limitation (assimilatory charge). An example of the routine and calculations are shown for one leaf and data are presented for leaves of 8-year-old-trees of two birch clones growing in Suonenjoki Forest Research Station, Finland, during summer 2000. Parameters Y CO2 , basic τ ′′ , a II , a I , K m (CO 2 ) and K s varied little in different leaves [relative standard deviation (RSD) < 7%], other parameters scattered widely (RSD typically 10‐40%). It is concluded that the little scattered parameters are determined by basic physico-chemical properties of the photosynthetic machinery whereas the widely scattered parameters are adjusting to growth conditions. The proposed non-destructive routine is suitable for diagnosing the photosynthetic machinery of leaves and may be applied in plant ecophysiology and in genetic engineering of plants.
Antiplatelet Effect of Leonurine from Leonurus sibiricus

Leonurine (1) was simply isolated from the aerial part of Leonurus sibircus var. albiflora. Their structures were established on the basis of spectral evidence. Leonurine showed a significant inhibited rabbit platelet aggregation induced by thrombin, arachidonic acid, and collagen in vitro with an IC50 of 97.22 μM, 31.03 μM, and 44.48 μM, respectively.
Ambient Stressors

The concept of "ambient stressor" is developed to address certain shortcomings in current formulations of environmental stress. Characteristics of ambient stressors are that they are chronic, negatively valued, nonurgent, physically perceptible, and intractable to the efforts of individuals to change them. Distinctions are drawn between the concepts of ambient stressors, acute stressors, and daily hassles. Particular attention is given to differences in psychological appraisals of ambient stressors and daily hassles. Factors are identified that influence appraisal processes (namely, characteristics of the contexts on which ambient stressors impinge) and personal, experiential influences. Additionally, the possible mediating effects of such factors on coping and ad-otation outcomes in response to ambient stressors are explored.
Nod1, an Apaf-1-like Activator of Caspase-9 and Nuclear Factor-κB*

Ced-4 and Apaf-1 belong to a major class of apoptosis regulators that contain caspase-recruitment (CARD) and nucleotide-binding oligomerization domains. Nod1, a protein with an NH2-terminal CARD-linked to a nucleotide-binding domain and a COOH-terminal segment with multiple leucine-rich repeats, was identified. Nod-1 was found to bind to multiple caspases with long prodomains, but specifically activated caspase-9 and promoted caspase-9-induced apoptosis. As reported for Apaf-1, Nod1 required both the CARD and P-loop for function. Unlike Apaf-1, Nod1 induced activation of nuclear factor-kappa-B (NF-κB) and bound RICK, a CARD-containing kinase that also induces NF-κB activation. Nod1 mutants inhibited NF-κB activity induced by RICK, but not that resulting from tumor necrosis factor-α stimulation. Thus, Nod1 is a leucine-rich repeat-containing Apaf-1-like molecule that can regulate both apoptosis and NF-κB activation pathways.
Climate predictability and breeding phenology in red deer: timing and synchrony of rutting and calving in Norway and France

Summary 1. Timing and synchrony of reproduction are regarded as crucially important factors for fitness in seasonal environments. Natural selection has probably favoured temperate and arctic female herbivores that match reproduction with onset of plant growth in spring. However, breeding synchrony may also be affected by variation in phenotypic quality of females in a population, because females in poor body condition have been found to delay ovulation and subsequent calving. 2. We compared breeding phenology, i.e. the timing and synchrony of rutting (roaring, sexual aggregation) and calving of red deer ( Cervus elaphus L.) in France (latitude: 49 ° N) and Norway (latitude: 63 ° N). We hypothesized (H 1 ) that calving and rutting were later at the site with latest onset of plant growth. 3. We further quantified overall environmental predictability as the sum of annual constancy and seasonality and tested three different (not mutually exclusive) hypotheses about breeding synchrony: (H 2a ) the population experiencing most seasonal plant phenology should show the highest breeding synchrony; (H 2b ) overall predictability of plant phenology should determine breeding synchrony; and (H 2c ) breeding should be more synchronized in the population with lowest female body weight variation within age classes because they ovulate more synchronously. 4. Calving and rutting, as well as onset of plant phenology, were later in Norway than in France, complying with the first hypothesis. Plant growth in spring was overall more predictable and also more seasonal in Norway than France. Hence we expected higher breeding synchrony in Norway than in France according to H 2a and H 2b . Variance in female body weight was slightly higher in France than in Norway, which should also cause more synchronized breeding in Norway than in France (H 2c ). Contrary to all predictions, variance in rutting and calving dates was around two times higher in Norway than in France. 5. We suggest two alternative explanations of breeding synchrony. A more variable topography in Norway can make optimal birth date more variable on a local scale than in France, thereby maintaining a higher genetic variance for calving date in Norwegian red deer. Further, population age structure may play a role, as ovulation varies according to female age. Clearly, processes of breeding synchrony are far more complex than previously realized.
PHOTOPERIODIC AND TEMPERATURE REGULATION OF DIAPAUSE IN LABIDOCERA AESTIVA (COPEPODA: CALANOIDA)

The calanoid copepod Labidocera aestiva was reared in the laboratory to as certain the effects of photoperiod and temperature on subitaneous and diapause egg production. The results indicate that photoperiod is the primary stimulus reg ulating the type(s) of eggs produced by a female, but that the temperature regimen can modify this effect. Under short daylength photoperiods (e.g., 8L: l6D) subi taneous egg production is increased by increasing the temperature regimen from 15. 0Â°Cor 19. 0Â°Cto 25. 0Â°C.However, under long daylength regimens (e.g., 18L:6D) females appear to be unresponsive to temperature changes within the range of 15. 0Â°C to 25. 0Â°C.It is suggested that this response to photoperiod and temperature more accurately couples the life cycle of L. aestiva with seasonal environmental fluctuations.
Selection of Winter Forage by Subarctic Browsing Vertebrates: The Role of Plant Chemistry

Plant palatability frequently moderates vertebrate herbivore forage selection patterns (e.g. 72, 73, 103, 104, 111, 137, 179, 195). There is, however, considerable debate as to which plant chemical characteristics control palatability (e.g. 9, 42, 110, 118, 120, 216). On the one hand, forage proximal nutritional quality is believed to be of primary importance (e.g. 18, 51, 103, 114, 130, 133, 137, 161, 173, 215). On the other, there is increasing speculation that forage selection patterns are largely the result of avoidance of plant secondary constituents that are antagonistic to vertebrate herbivore fitness (e.g. 1, 2, 9, 12, 25, 49, 112, 116, 120, 141, 153, 165, 199, 200). In this paper we examine these alternatives for a specific system. We consider the interface between subarctic browsing vertebrates and woody browse plants during winter and attempt to answer the following questions: During winter do subarctic browsing vertebrates (a) feed preferentially upon plant tissues that contain relatively high concentrations of proximal nutrients or energy, or (b) consistently avoid plant tissues that
INACTIVATION OF CELL MOVEMENT FOLLOWING SEXUAL CELL RECOGNITION IN PARAMECIUM CAUDATUM

A positive correlation between sexual cell recognition and decrease in swimming velocity was studied in the ciliated protozoan, Paramecium caudatum. Ciliary membrane vesicles with conjugation-inducing activity rapidly decreased swimming velocity of living cells of the opposite mating type. Immobilization of the ventral cilia and perturbation of metachronal waves in the dorsal cilia were observed upon application of the membrane vesicles. Anterior shift of the beating direction and decrease in the beating angle or amplitude were also observed in the cells reacting to the vesicles. A similar change of swimming behavior and ciliary inactivation was seen in the chemical induction of conjugation. A possible regulatory mechanism of ciliary movement is discussed.
A study of the digestion of protein in humans using ileal and faecal assays : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in biochemistry at Massey University

A study was conducted with 12 adult human subjects including six ilecstomates, to determine the digestibility of protein in a single mixed diet. Significant {P<0.05) differences were found between ileal and faecal amino acid digestibility values for most aDi~o acids {histidine, arginine, aspartate, threonine, serine, glycine, proline, valir.e, leucine, phenylalanine, methionine, cysteine and tryptophan). The ileal digestibility coefficients ranged from 71.5 to 93.6% fer glycine and lysine, respectively, whereas the faecal values ranged from 77.9 to 94.7% for glycine and leucine, respectively. The absolute differences between the methods ranged from 0.2 to 15.0% units for alanine/isoleucine and glycine respectively, and the average of the differences was 3.7% units. The ileosto~ised growing pig {25kg) was investigated as a model animal to allow more routine determination of the ileal digestibility of protein in human foods, and good agreement was found between the species for apparent ileal amino acid digestibility. T~ere were no significant differences between the two species for the apparent ileal amino acid digestibilities of amino acids, except for lysine, glutamate, proline and alanine. The endogenous flows of amino acids at the terminal ileum were determined in both species, following consumption of a single protein-free meal. The amino acid ccmpositions of the protein flows were similar for pigs and humans, with significant differences only being found for histidine, threonine, alanine, valine and methionine. The endogenous flows were used to correct apparent coefficients to give true estimates of digestibility. The latter values indicated near complete absorption of the dietary ami~o acids for the human subjects and growing pigs. When the interspecies comparison was based on the true digestibility values, there were only significant differences for the amino acids glutamate, phenylalanine, cysteine and methionine. The absolute differences
A Large Scale Study on Health Information Retrieval for Laypersons

In the time of COVID-19, people has rigid demand on seeking accurate health information from internet. However, health information searching is still a challenge in information retrieval (IR) technology and real-world medical informatics applications. To improve healthcare, many medical search engines have been built based on natural language processing, machine learning, and other computational techniques to address related IR problems, but the result have not always been satisfactory, especially to laypersons, because those information access tools cannot, for example, retrieve documents with high relevance and support people’s need.On the country, models based on IR produce a relatively ideal performance on relevance, readability, and credibility.Therefore, IR technology has become popular and widespread. The work addressed three aims: First, I implemented a BM25-based IR model with a query expansion using the REINFORCE algorithm on a benchmark dataset, called clefehealth2018_B released as part of the CLEF eHealth Lab by the Conference and Labs of the Evaluation Forum. Second, I compared my method with the baseline. Third, as one of the organisers of this year’s CLEF eHealth IR Task, I set up a website-based evaluation tool for manually labelling submitted documents from participants. In the experiments, the new method achieved a better performance than the baseline with the best Precision@10 and NDCG@10 scores being 0.534 and 0.492, respectively. The results gave evidence of the proposed method being able to return more relevant documents and the primary information extraction operation in the data pre-processing improved the model performance further. The novelty of the research was training the REINFORCE algorithm based reformulator for query expansion. Furthermore, the detailed comparisons between different searching engines and various settings were illustrated. Finally, this work resulted in a new IR idea to further study on the benchmark dataset using a reinforcement learning method to expand queries.
Current Understanding of Mycobacterium abscessus Infection

Mycobacterium abscessus belongs to a group of rapidly growing mycobacteria (RGM) that cause a broad spectrum of infections in humans. In addition, the association of M. abscessus with the cause of community- and hospital-acquired infections has been recently reported. In fact, M. abscessus is known to be the most drug-resistant mycobacterium and naturally resistant to first-line anti-tuberculous drugs, resulting in the limited therapeutic options and a high failure rate of treatment response. Three closely related species; M. abscessus (sensu stricto), M. bolletii, and M. massiliense are currently identified however, consensus on the naming of M. abscessus-related species has not been made to date. We herein discuss the advanced understanding of the virulence potentials and pathophysiological features of M. abscessus to establish novel therapeutic strategies for M. abscessus infection.
Bioavailability of quercetin from flesh scales and dry skin of onion in rats.

Quercetin is a natural compound widely distributed in the plant food. It is still not certain which forms of quercetin, aglycone or glycosides, are better bioavailable. In this study, for the first time, the bioavailability of quercetin and quercetin β-glucosides was compared from dietary sources. As a source of quercetin glucosides, two outer fleshy onion scales of B³onska variety containing 21.30 mg Q/g d.m. (99.3% of quercetin as glucosides) were used, while quercetin aglycone originated from onion dry skin of the same variety containing 34.80 mg Q/g d.m. (53.2 % of quercetin as aglycone). The results showed that bioavailability of quercetin glucosides was 50% of that of quercetin aglycone (p ≤ 0.05). A factor which may be the reason for differences in the determined bioavailabilities are the mechanisms of transportation and hydrolysis. It is suggested that more hydrophobic quercetin may pass through biological membranes to reach intestinal enterocytes via passive transport, while for more polar quercetin glucosides two mechanisms are proposed: prior to absorption they may be hydrolyzed in the intestinal lumen by β-glucosidases and released free quercetin is absorbed as above, or they may enter enterocytes via Na+/glucose transporter.