bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature acclimation affects thermal preference and tolerance in three Eremias lizards (Lacertidae)
Authors: Li Hong , Wang Zheng , Mei Wenbin , Ji Xiang
Published: September 2019

We acclimated adult males of three Eremias lizards from different latitudes to 28°C, 33 °C or 38°C to examine whether temperature acclimation affects their thermal preference and tolerance and whether thermal preference and tolerance of these lizards correspond with their latitudinal distributions. Overall, selected body temperature (Tsel) and viable temperature range (VTR) were both highest in E. brenchleyi and lowest in E. multiocellata, with E. argus in between; critical thermal minimum (CTMin) was highest in E. multiocellata and lowest in E. brenchleyi, with E. argus in between; critical thermal maximum (CTMax) was lower in E. multiocellata than in other two species. Lizards acclimated to 28°C and 38 °C overall selected lower body temperatures than those acclimated to 33°C; lizards acclimated to high temperatures were less tolerant of low temperatures, and vice versa; lizards acclimated to 28 °C were less tolerant of high temperatures but had a wider VTR range than those acclimated to 33°C and 38°C. Lizards of three species acclimated to the three temperatures always differed from each other in CTMin, but not in Tsel, CTMax and VTR. Our results show that: temperature acclimation plays an important role in influencing thermal preference and tolerance in the three Eremias lizards, although the degrees to which acclimation temperature affects thermal preference and tolerance differ among species; thermal preference rather than tolerance of the three Eremias lizards corresponds with their latitudinal distributions.
How do soil fauna and soil microbiota respond to beech forest growth?
Authors: Chauvat Matthieu , Zaitsev Andrei S. , Gabriel Ernst , Wolters Volkmar
Published: September 2019

The dynamics and performance of soil biota during forest rotation were studied in monoculture beech stands forming a chronosequence of four different age-classes (30, 62, 111, 153 yr). Biomass was monitored in major groups of microflora, microfauna, mesofauna, and macrofauna. Resource availability (litter layer, soil organic mater), biomass of the two dominant decomposer groups (microflora, earthworms) as well as the biomass of mesofauna and microfauna were found to remain quite stable during forest succession. Nevertheless, the marked increase of the biomasses of primary decomposers (fungi, saprophagous macroinvertebrates) in the 62-year-old stand, followed by an increase of the biomasses of macropredators in the 111-year-old stand, indicate substantial changes of several components of edaphic communities during forest development. However, constant values of soil respiration suggest that the overall performance of the soil food web does not change during beech forest succession. Thus, the decomposer system of lowland managed beech forests on calcareous soils seems to be very stable over time. We suggest that earthworm activity might have masked impacts of forest development on other soil biota and led to an astounding stability of decomposer assemblages during beech forest rotation.
Cloning, characterization of two female-specific AFLP markers and development of PCR-based sex identification method for the half-smooth tongue sole Cynoglossus semilaevis
Authors: Ma Hongyu , Chen Songlin , Li Jing , Bi Jin-Zhen , Xu Tianjun
Published: September 2019

Two female-specific AFLP (amplified fragment length polymorphism) markers (named CseF464 and CseF136) were isolated by using one selective primer combination (E-AGC/M-CTG) from the genomic DNA of 20 females and 20 males of the half-smooth tongue sole Cynoglossus semilaevis. Both the markers were re-amplified, recovered from the agarose gels, cloned and sequenced. Bioinformatics analysis indicated that the length of the two markers were 468 bp and 134 bp, respectively, and the sequences showed no similarity to each other, as well as to the known sequences deposited in the GenBank database using BLASTn. Two pairs of SCAR (sequence characterized amplified regions) primers were designed based on the sequences of the two female-specific markers. Furthermore, PCR-based genetic sex identification method was developed in Cynoglossus semilaevis. A specific fragment was amplified in all females but not in any males by using these SCAR primers on the initial 20 female and 20 male individuals of Cynoglossus semilaevis. The feasibility of the two SCAR primer pairs was confirmed in additional 100 individuals (50 females and 50 males). This allowed for reliable, rapid molecular identification of genetic sex of the species, genetic mapping on the sex chromosomes and better understanding of the sex determination and sex differentiation in the half smooth tongue sole.
Restoration of sea eagle population: A review
Authors: Rajchard Josef , Procházka Jan
Published: September 2019

The population density of the white-tailed sea eagle Haliaeetus albicilla is very low in many countries. In last twenty years, the sea eagle population in South Bohemia was restored by strict protection subsidized by reintroduction. The active help consisted of feeding during winter and building of artificial nests. A new sea eagle breeding population arose in the Třeboň basin area in the early 1980’s. Until this time sea eagles had used former breeding places only for wintering, probably coming from the Baltic. The South Bohemian sea eagle population is very unique: it exists in a densely man-occupied landscape, mainly in areas with very intensive carp breeding in artificial fishponds and was partly artficially (help to wintering birds and reintroduction of some individuals) restored. The experience from South Bohemia may have importance for populations of the sea eagle in other areas of its occurence, primarily in the continental conditions
Efficient production of transgenic chickens using self-inactive HIV-based lentiviral vectors
Authors: Xu Shiyong , Sun Yan , Ding Hongmei , Wang Meng , Cai Yafei , Chen Jie , Liu Honglin
Published: September 2019

We demonstrated the simple and effective production of transgenic chickens, in which the enhanced green fluorescence protein (EGFP) was expressed by using third-generation self-inactive HIV-based lentiviral vectors. In our experiments, lentiviruses were injected into 204 fertilized eggs, from which 30 (15%) chickens were hatched. The exogenous gene was detected in the genomes of 16 out of 30 (53%) chickens. The green fluorescence signal was observed directly in various body parts, and was particularly significant in the testes. The transgenes were also found in the offspring of these chickens. The results indicate that HIV-based lentiviral vectors can be used to generate transgenic birds economically and effectively
Susceptibility of pine stands to bark stripping by chacma baboons Papio ursinus in the Eastern Highlands of Zimbabwe
Authors: Katsvanga C.A.T. , Jimu L. , Mupangwa J.F. , Zinner D.
Published: September 2019

The aim of this study was to determine the susceptibility, intensity and distribution of pine trees to bark stripping by chacma baboons Papio ursinus in three plantations in the Eastern Highlands of Zimbabwe. The number of plots/ha, stripped trees/plot and stripped trees/ha was recorded during the pre-rainy, rainy and post-rainy seasons from August 2006 to May 2007. During data collection, altitude, aspect, season and other site predictor variables (e.g., roads and fire traces, water points, indigenous vegetation conservation areas, crop fields, human settlements, wattle scrubs, rocky areas, open grasslands, earlier stripped sites and roost sites) were recorded for each plot in association with selected predictor variables within plantation estates. Data on the number of stripped plots/ha, stripped trees/plot and stripped trees/ha were analysed as dependent variables using the Generalised linear Model (GLM) through SPSS version 15 (2006) to determine which predictor variables were significantly related to bark stripping. Differences between means were tested using Bonferroni tests with a 5% level of significance. Our findings show that bark stripping of pine trees by baboons occurred at all altitudes and aspects. Overall, the number of bark stripped trees/ha did not significantly vary by season. The number of bark stripped plots/ha was lower during the pre-rainy season than the rainy season, whereas the number of bark stripped trees/plot was higher during the pre-rainy than the rainy season. Bark stripping of pines occurred more often in the vicinities of areas with abundant food and water.
Homozygous lethality and heterozygous spotting due to a novel missense mutation in the mouse Kit gene
Authors: Wu Baojin , Yin Lijing , Yin Xiaoshu , Yang Weiwei , Chen Bing , Xue Zhengfeng , Wu Peilin
Published: September 2019

N-ethyl-N-nitrosourea (ENU) mutagenesis in mice can be used to study gene function in vivo and to establish genetic mouse models of human disease. In this study, a white spotted mouse (named KitW-1 Bao) was obtained by ENU-induced mutagenesis. Inheritance testing showed a single-gene dominant mutation and lethality in the KitW-1 Bao homozygous mice. The mutation was mapped to Chromosome 5 between markers D5 Mit356 and D5 Mit308. The region contains the Kit gene, whose mutations are known to lead to pigmentation defects in mice. Sequence analysis of the Kit cDNA from KitW-1 Bao heterozygotes revealed an A to T missense mutation resulting in an amino acid substitution of Asp (D) by Val (V) at amino acid position 849 within a highly conserved tyrosine kinase domain. The combined phenotype displayed by the KitW-1 Bao heterozygous and homozygous mutant mice demonstrates the critical function of the highly conserved aspartic acid residue at position 849 in the Kit gene product.
Assessing feeding competition between lake whitefish Coregonus clupeaformis and round whitefish Prosopium cylindraceum
Authors: Macpherson Andrew , Holmes John A. , Muir Andrew M. , Noakes David L. G.
Published: September 2019

We collected lake whitefish Coregonus clupeaformis and round whitefish Prosopium cylindraceum from the main basin of Lake Huron and Georgian Bay in the Laurentian Great Lakes of North America to investigate details of diet and feeding tactics of these species in different seasons. Lake whitefish supports important commercial fisheries in Lake Huron and both species make use of habitats near the Bruce Nuclear Power Development, on the eastern shore of Lake Huron. Most fish of both species showed generalist feeding behavior, but some lake whitefish appeared to show specialist prey selection. The invasive spiny water flea Bythotrephes longimanus was an important component of the diet of both species. There was considerable dietary overlap between the whitefish species, but the ecological implications of these dietary overlaps are mitigated by the fact that dominant prey species differed in most seasons. We conclude that the potential for ecologically significant interactions between lake whitefish and round whitefish resulting from competition for similar benthic food resources in the main basin of Lake Huron is probably low.
Factors influencing the establishment of dominance hierarchies of the grey triggerfish Balistes capriscus
Authors: Cleveland David W. , Lavalli Kari L.
Published: September 2019

Unlike other balistids, grey triggerfish Balistes capriscus occur in social groups in subtropical reef assemblages and have been noted to cooperate in capturing large crustacean prey. The objective of this study were to determine the structure of dominance hierarchies of these social groups and the factors that influence hierarchies of wild-caught grey triggerfish in a naturalistic setting. From observations of four groups of triggerfish (n = 19 fish) in both dyad and group (4 - 5 fish) settings, we provide a description of triggerfish behaviors and coloration patterns and an explanation of the social context in which suites of behaviors are used by dominant, middle-ranking, and subordinate fish. Sixteen behaviors and nine coloration patterns were noted for grey triggerfish. Grey triggerfish groups form linear hierarchies in both dyads and groups as measured by Landau's Index of Linearity (h = 1.0 for Groups 1, 3, and 4 and h = 0.95 for Group 2 in dyads; h = 1.0 for all groups in group settings). Dyadic hierarchies, however, were not necessarily good predictors of the hierarchies found in larger group settings, as they only predicted two of the four group hierarchies. Sex played no role in influencing status or behavior. Size had the greatest influence on dominance status, with larger fish being more dominant than smaller fish. An individual's dominance ranking influenced both body coloration and posture. These results suggest that color patterns and body postures may also be used by observers as an indicator of an individual's social status in groups.
The foraging behavior of Japanese macaques Macaca fuscata in a forested enclosure: Effects of nutrient composition, energy and its seasonal variation on the consumption of natural plant foods
Authors: Jaman M. Firoj , Huffman Michael A. , Takemoto Hiroyuki
Published: September 2019

In the wild, primate foraging behaviors are related to the diversity and nutritional properties of food, which are affected by seasonal variation. The goal of environmental enrichment is to stimulate captive animals to exhibit similar foraging behavior of their wild counterparts, e.g. to extend foraging time. We conducted a 12-month study on the foraging behavior of Japanese macaques in a semi-naturally forested enclosure to understand how they use both provisioned foods and naturally available plant foods and what are the nutritional criteria of their consumption of natural plants. We recorded time spent feeding on provisioned and natural plant foods and collected the plant parts ingested of their major plant food species monthly, when available. We conducted nutritional analysis (crude protein, crude lipid, neutral detergent fiber-‘NDF’, ash) and calculated total non-structural carbohydrate – ‘TNC’ and total energy of those food items. Monkeys spent 47% of their feeding time foraging on natural plant species. The consumption of plant parts varied significantly across seasons. We found that leaf items were consumed in months when crude protein, crude protein-to-NDF ratio, TNC and total energy were significantly higher and NDF was significantly lower, fruit/nut items in months when crude protein and TNC were significantly higher and crude lipid content was significantly lower, and bark items in months when TNC and total energy were higher and crude lipid content was lower. This preliminary investigation showed that the forested enclosure allowed troop members to more fully express their species typical flexible behavior by challenging them to adjust their foraging behavior to seasonal changes of plant item diversity and nutritional content, also providing the possibility for individuals to nutritionally enhance their diet.
Lamprey buccal gland secretory protein-2 (BGSP-2) inhibits human T lymphocyte proliferation
Authors: Sun Jing , Yu Shuiyan , Xue Zhuang , Liu Cenjie , Wu Yu , Liu Xin , Li Qingwei
Published: September 2019

Lamprey is a representative of the agnathans, the most ancient class of vertebrates. Parasitic lampreys secrete anticoagulant from their buccal glands and prevent blood coagulation of host fishes. We identified a buccal gland secretory protein-2 (BGSP-2) from a buccal gland cDNA library of Lampetra japonica. The full-length BGSP-2 gene was cloned and the recombinant BGSP-2 protein was generated. The role of BGSP-2 on lymphocyte proliferation was studied by examining its effects on human T lymphocytes. We found that lamprey BGSP-2 was able to effectively block the proliferation of T cells in vitro by inducing G1/S cell cycle arrest. Furthermore, it inhibited the proliferation of human T lymphocytes stimulated by phytohemagglutinin (PHA) at a minimum concentration of 0.μg/ml. Our data suggest that lamprey BGSP-2 is able to block the mitosis of human T lymphocytes at the G1/S point, and has the potential of anti-proliferative effect on PHA-activated T lymphocytes.
Female mate choice and the potential for ornament evolution in túngara frogs Physalaemus pustulosus
Authors: Ryan Michael J. , Bernal Ximena E. , Rand A. Stanley
Published: September 2019

The potential for ornament evolution in response to sexual selection rests on the interaction between the permissiveness or selectivity of female preferences and the constraints on male development of signaling related traits. We investigate the former by determining how latent female preferences either exaggerate the magnitude of current traits (i.e. elaborations) or favor novel traits (i.e. innovations). In túngara frogs, females prefer complex mating calls (whine-chucks) to simple calls (whine only). The whine is critical for mate recognition while the chuck further enhances the attractiveness of the call. Here we use a combination of synthetic and natural stimuli to examine latent female preferences. Our results show that a diversity of stimuli, including conspecific and heterospecific calls as well as predator-produced and human-made sounds, increase the attractiveness of a call when added to a whine. These stimuli do not make simple calls more attractive than a whine-chuck, however. In rare cases we found stimuli that added to the whine decrease the attractiveness of the call. Overall, females show strong preferences for both elaborations and innovations of the chuck. We argue that the emancipation of these acoustic adornments from mate recognition allows such female permissiveness, and that male constraints on signal evolution are probably more important in explaining why males evolved their specific adornment. Experimentally probing latent female preferences for stimuli out of the species‘ range is a useful means to gain insights about the potential of female choice to influence signal evolution and thus the astounding diversity in male sexually-selected traits.
Habitat relationships of reptiles in pine beetle disturbed forests of Alabama, U.S.A. with guidelines for a modified drift-fence sampling method
Authors: Sutton W. B. , Wang Y. , Schweitzer C. J.
Published: September 2019

Understanding vertebrate habitat relationships is important to promote management strategies for the longterm conservation of many species. Using a modified drift fence method, we sampled reptiles and compared habitat variables within the William B. Bankhead National Forest (BNF) in Alabama, U.S.A from April 2005 to June 2006. We captured 226 individual reptiles representing 19 species during 564 total trap nights. We used canonical correspondence analysis to examine habitat associations for the reptiles sampled and we detected a distinct habitat gradient ranging from sites with greater litter depth and percent canopy cover to more open sites with greater woody, herbaceous, and coarse woody debris (CWD) coverage, and CWD volume. Little brown skinks Scincella lateralis and eastern worm snakes Carphophis a. amoenus were associated with sites with greater litter depth and canopy cover, whereas eastern fence lizards Sceloporus undulatus, copperheads Agkistrodon contortrix, and gray ratsnakes Pantherophis spiloides were associated with sites possessing greater CWD coverage and volume. We found that disturbances due to the southern pine beetle Dendroctonus frontalis were likely important for influencing reptile distributions through the creation of canopy gaps and fallen coarse woody debris. Compared to other studies, our modified drift-fence trap technique was successful for sampling larger snake species (66 snakes in 564 trap nights). We have also provided detailed schematics for constructing drift fence array and box traps used in this study.
Central pattern generation underlying Limulus rhythmic behavior patterns
Authors: Wyse Gordon A.
Published: September 2019

Many behavioral activities of the horseshoe crab Limulus are rhythmic, and most of these are produced in large part by central pattern generators within the CNS. The chain of opisthosomal ('abdominal') ganglia controls gill movements of ventilation and gill cleaning, and the prosomal ring of fused ganglia (brain and segmental 'thoracic' ganglia) controls generation of feeding and locomotor movements of the legs. Both the opisthosomal CNS and the prosomal CNS can generate behaviorally appropriate patterns of motor output in isolation, without movements or sensory input. Preparations of the isolated opisthosomal CNS generate rhythmic output patterns of motor activity characterized as fictive ventilatory and gill cleaning rhythms. Moreover, CNS preparations also express longer-term patterns, such as intermittent ventilation or sequential bouts of ventilation and gill cleaning. Such longer-term patterns are commonly observed in intact animals. The isolated prosomal CNS does not spontaneously generate the activity patterns characteristic of walking, swimming, and feeding. However, perfusion of octopamine in the isolated prosomal CNS activates central pattern generators underlying rhythmic chewing movements, and injection of octopamine into intact Limulus promotes the chewing pattern of feeding, whether or not food is presented. Our understanding of the ability of neuromodulators such as octopamine to elicit or alter central motor programs may help to clarify the central neural circuits of pattern generation that produce and coordinate these rhythmic behaviors.
High resolution tracking of adult horseshoe crabs Limulus polyphemus in a New Hampshire estuary using fixed array ultrasonic telemetry
Authors: Watson Winsor H. , Chabot Christopher C.
Published: September 2019

While several studies have documented the large-scale, seasonal movements of horseshoe crabs, little is known about their fine-scale, daily movement patterns. In this study we used a fixed array ultrasonic telemetry system to track the movements of 12 male and 16 female horseshoe crabs in the Great Bay estuary, New Hampshire. Data were obtained during the mating season, as well as during the remainder of the summer and fall, in the years 2005-2008. During the mating season animals were often, but not always, active during the high tides when they were approaching and leaving the spawning beaches. On average, both males and females approached mating beaches during 33% of the high tides they experienced and they most often made the transition from being inactive to active during the last two hours of an incoming tide. From April-October horseshoe crabs were significantly more active during high tide periods vs low tide periods, with no clear preference for diurnal vs nocturnal activity. After the mating season ended horseshoe crabs continued to move into shallower water at high tide and then return to deeper water at low tide. Observations by SCUBA divers suggest that during these excursions into the mudflats horseshoe crabs were digging pits in the sediment while foraging for food. Thus, the tidal rhythm of activity that has been so well documented during the mating season probably persists into the fall, and primarily involves foraging activities.
Orientation of larval and juvenile horseshoe crabs Limulus polyphemus to visual cues: Effects of chemical odors
Authors: Medina Julie M. , Tankersley Richard A.
Published: September 2019

Adult horseshoe crabs Limulus polyphemus have long served as models for the study of vision in marine arthropods. Yet, little is known about the ability of early life history stages to detect and respond to visual cues. We examined the visually directed movements of larvae and first stage juveniles to horizons containing dark visual targets of different sizes. The study tested the hypotheses that (1) larval and juvenile crabs can detect and respond to visual targets and (2) the direction of orientation varies with the presence of chemical cues associated with settlement habitats. Orientation of larval and juvenile crabs to rectangles subtending angles from 30–330° was tested in a circular arena containing water that either lacked estuarine chemical cues (offshore water) or contained odors from aquatic vegetation or known predators. In the absence of chemical odors, larvae oriented toward and juveniles moved away from dark horizons subtending angles > 60°. When placed in water containing chemical odors from potential nursery habitats, including the seagrasses Halodule wrightii and Syringodium filiforme, crabs reversed their direction of orientation relative to their responses in offshore water. Odors from two known predators, the mummichug Fundulus grandis and blue crab Callinectes sapidus, had no affect on the orientation of larvae. Yet, juveniles responded to both odors by moving toward the visual target. Results support the hypothesis that the visual orientation of larval and juvenile horseshoe crabs changes upon exposure to habitat and predator cues and that the direction of the response undergoes an ontogenetic shift following metamorphosis.
Activity budget of Rhinopithecus bieti at Tibet: Effects of day length, temperature and food availability
Authors: Xiang Zuofu , Huo Sheng , Xiao Wen
Published: September 2019

How animals allocate their time to various activities has significant consequences for their survival because they reflect the different constraints on time-energy balances. Many ecological variables, such as day length, temperature, food availability, are supposed to effect on activity budgets allocation of temperate primates. To examine the potential influence of these three variables, the activity budgets of Rhinopithecus bieti was studied at Xiaochangdu, Tibet from June 2003 to March 2005. Pearson correlations were utilized to assess potential relationships between activity budget and day length, food availability and temperature, and stepwise multiple regressions to identify the priority of resting and other activities (activities besides feeding, moving and resting). Time spent resting and doing "other activities" is positively related to day length, temperature and food availability. No significant correlations were found between feeding/moving time and any of these variables. This suggests that foraging time (feeding + moving) takes priority over rest and other activities. Day length and foraging time (as independent variables) were related to the time spent in the other two activities besides feeding/moving (as dependent variables). Both time spent resting and in "other activities" were highly significant positive functions of day length, with the latter a highly significant negative function of feeding time and moving time. Resting time may therefore be interpreted as taking priority over "other activities" time. These results provide further evidence of the importance of day length, temperature and food availability to seasonal activity budgets .
Loss of CO2 sensing by the olfactory system of CNGA3 knockout mice
Authors: Han Jinlong , Luo Minmin
Published: September 2019

Atmospheric CO2 can signal the presence of food, predators or environmental stress and trigger stereotypical behaviors in both vertebrates and invertebrates. Recent studies have shown that the necklace olfactory system in mice sensitively detects CO2 in the air. Olfactory CO2 neurons are believed to rely on cyclic guanosine monophosphate (cGMP) as the key second messenger; however, the specific ion channel underlying CO2 responses remains unclear. Here we show that CO2-evoked neuronal and behavioral responses require cyclic nucleotide-gated (CNG) channels consisting of the CNGA3 subunit. Through Ca2+-imaging, we found that CO2-triggered Ca2+ influx was abolished in necklace olfactory sensory neurons (OSNs) of CNGA3-knockout mice. Olfactory detection tests using a Go/No-go paradigm showed that these knockout mice failed to detect 0.5% CO2. Thus, sensitive detection of atmospheric CO2 depends on the function of CNG channels consisting of the CNGA3 subunit in necklace OSNs. These data support the important role of the necklace olfactory system in CO2 sensing and extend our understanding of the signal transduction pathway mediating CO2 detection in mammals.
Variation benchmark datasets: update, criteria, quality and applications
Authors: Sarkar Anasua , Yang Yang , Vihinen Mauno
Published: September 2019

Development of new computational methods and testing their performance has to be carried out using experimental data. Only in comparison to existing knowledge can method performance be assessed. For that purpose, benchmark datasets with known and verified outcome are needed. High-quality benchmark datasets are valuable and may be difficult, laborious and time consuming to generate. VariBench and VariSNP are the two existing databases for sharing variation benchmark datasets used mainly for variation interpretation. They have been used for training and benchmarking predictors for various types of variations and their effects. VariBench was updated with 419 new datasets from 109 papers containing altogether 329 014 152 variants; however, there is plenty of redundancy between the datasets. VariBench is freely available at http://structure.bmc.lu.se/VariBench/. The contents of the datasets vary depending on information in the original source. The available datasets have been categorized into 20 groups and subgroups. There are datasets for insertions and deletions, substitutions in coding and non-coding region, structure mapped, synonymous and benign variants. Effect-specific datasets include DNA regulatory elements, RNA splicing, and protein property for aggregation, binding free energy, disorder and stability. Then there are several datasets for molecule-specific and disease-specific applications, as well as one dataset for variation phenotype effects. Variants are often described at three molecular levels (DNA, RNA and protein) and sometimes also at the protein structural level including relevant cross references and variant descriptions. The updated VariBench facilitates development and testing of new methods and comparison of obtained performances to previously published methods. We compared the performance of the pathogenicity/tolerance predictor PON-P2 to several benchmark studies, and show that such comparisons are feasible and useful, however, there may be limitations due to lack of provided details and shared data.

Database URL: http://structure.bmc.lu.se/VariBench
Footprints and Ootheca of Lycorma delicatula Influence Host-Searching and -Acceptance of the Egg-Parasitoid Anastatus orientalis
Authors: Malek Robert , Kaser Joe M , Broadley Hannah J , Gould Juli , Ciolli Marco , Anfora Gianfranco , Hoelmer Kim A
Published: September 2019

The spotted lanternfly, Lycorma delicatula White (1845) (Hemiptera: Fulgoridae), is an invasive insect that was first reported in North America in Berks County, Pennsylvania, in 2014. It is a polyphagous phloem feeder that attacks over 70 plant species, threatening the agricultural, lumber, and ornamental industries of North America. Infestations of the pest have been reported in several U.S. counties, and a lack of endemic predators and parasitoids feeding on L. delicatula suggests a release from natural enemies in the invaded range. An egg-parasitoid Anastatus orientalis (Hymenoptera: Eupelmidae) was reported attacking L. delicatula at high rates in its native range and may play a key role in reducing its populations there. To better understand the foraging behavior of A. orientalis, a series of behavioral experiments were conducted to determine successful parasitism and behavioral responses to traces left by adult L. delicatula and to the oothecae which cover their eggs. Our results suggest that wasps detected chemical traces left by L. delicatula adults while walking on surfaces and exhibited a strong arrestment response. Moreover, wasps preferred to oviposit in egg masses with intact oothecae. The implications of these findings are herein discussed with regard to the exploitation of host kairomones by foraging wasps, as well as to its ability to overcome host structural defenses.
How does the duration of consults vary for upper respiratory tract infections in general practice where an antibiotic has been prescribed?
Authors: Darlison Shepherd Phoebe R , Krejany Catherine J , Jiwa Moyez
Published: September 2019

Background

There is limited data on the duration of consults resulting in the prescription of antibiotics for upper respiratory tract infections (URTIs) in general practice.

Objective

To explore how demographic factors influence consult duration where antibiotics have been prescribed for URTI in Australian general practice.

Methods

2985 URTI-specific presentations were identified from a national study of patients who were prescribed an antibiotic after presenting to general practice between June and September 2017. Consult duration was analysed to assess for any variation in visit length based on demographic factors.

Results

The overall median consult duration was 11.42 minutes [interquartile range (IQR) 7.95]. Longer consult duration was associated with areas of highest socio-economic advantage where patients living in postcodes of Index of Relative Socio-economic Advantage and Disadvantage (IRSAD) Quintile 5 (highest 20% on the IRSAD) had significantly longer consults [median 13.12 (IQR 8.01)] than all other quintiles (P < 0.001). Females [11.75 (IQR 8.13)] had significantly longer consults than males [10.87 (IQR 7.57); P < 0.001]. Clinics based in State C and State F had significantly shorter consults when compared with all other included states and territories (P < 0.001) and shorter consult duration was associated with visits on Sundays [median 8.18 (IQR 5.04)].

Conclusion

There is evidence for the association of demographic and temporal factors with the duration of consultations for URTIs where an antibiotic has been prescribed. These factors warrant further research.
Transcriptional signatures of Mycobacterium tuberculosis in mouse model of intraocular tuberculosis
Authors: Abhishek Sudhanshu , Ryndak Michelle Beth , Choudhary Alpa , Sharma Sumedha , Gupta Amod , Gupta Vishali , Singh Nirbhai , Laal Suman , Verma Indu
Published: September 2019

Background

Studies on human intraocular tuberculosis (IOTB) are extremely challenging. For understanding the pathogenesis of IOTB, it is important to investigate the mycobacterial transcriptional changes in ocular environment.

Methods

Mice were challenged intravenously with Mycobacterium tuberculosis H37Rv and at 45 days post-infection, experimental IOTB was confirmed based on bacteriological and molecular assays. M. tuberculosis transcriptome was analyzed in the infected eyes using microarray technology. The identified M. tuberculosis signature genes were further validated and investigated in human IOTB samples using real-time polymerase chain reaction.

Results

Following intravenous challenge with M. tuberculosis, 45% (5/12) mice showed bacilli in the eyes with positivity for M. tuberculosis ribonucleic acid in 100% (12/12), thus confirming the paucibacillary nature of IOTB similar to human IOTB. M. tuberculosis transcriptome in these infected eyes showed significant upregulation of 12 M. tuberculosis genes and five of these transcripts (Rv0962c, Rv0984, Rv2612c, Rv0974c and Rv0971c) were also identified in human clinically confirmed cases of IOTB.

Conclusions

Differentially expressed mycobacterial genes identified in an intravenously challenged paucibacillary mouse IOTB model and presence of these transcripts in human IOTB samples highlight the possible role of these genes for survival of M. tuberculosis in the ocular environment, thus contributing to pathogenesis of IOTB.
Effect Size Guidelines, Sample Size Calculations, and Statistical Power in Gerontology
Authors: Brydges Christopher R
Published: September 2019

Background and Objectives

Researchers typically use Cohen’s guidelines of Pearson’s r = .10, .30, and .50, and Cohen’s d = 0.20, 0.50, and 0.80 to interpret observed effect sizes as small, medium, or large, respectively. However, these guidelines were not based on quantitative estimates and are only recommended if field-specific estimates are unknown. This study investigated the distribution of effect sizes in both individual differences research and group differences research in gerontology to provide estimates of effect sizes in the field.

Research Design and Methods

Effect sizes (Pearson’s r, Cohen’s d, and Hedges’ g) were extracted from meta-analyses published in 10 top-ranked gerontology journals. The 25th, 50th, and 75th percentile ranks were calculated for Pearson’s r (individual differences) and Cohen’s d or Hedges’ g (group differences) values as indicators of small, medium, and large effects. A priori power analyses were conducted for sample size calculations given the observed effect size estimates.

Results

Effect sizes of Pearson’s r = .12, .20, and .32 for individual differences research and Hedges’ g = 0.16, 0.38, and 0.76 for group differences research were interpreted as small, medium, and large effects in gerontology.

Discussion and Implications

Cohen’s guidelines appear to overestimate effect sizes in gerontology. Researchers are encouraged to use Pearson’s r = .10, .20, and .30, and Cohen’s d or Hedges’ g = 0.15, 0.40, and 0.75 to interpret small, medium, and large effects in gerontology, and recruit larger samples.
Are We There Yet? Immersive Virtual Reality to Improve Cognitive Function in Dementia and Mild Cognitive Impairment
Authors: Sayma Meelad , Tuijt Remco , Cooper Claudia , Walters Kate
Published: September 2019

Background and Objectives

Cognitive training therapies may delay cognitive deterioration in dementia. There is potential to enhance delivery through immersive virtual reality (IVR), as removing potential distractors for cognitively impaired individuals can enhance their experience, resulting in increased engagement. Evidence in this field is emerging and not yet synthesized. We aimed to summarize research investigating the use of IVR in dementia to evaluate the current extent of use, acceptability, feasibility, and potential effectiveness. We also aimed to identify gaps in current research and to create a set of recommendations in utilizing this therapy.

Research Design and Methods

A systematic literature review was conducted. Our review was registered with PROSPERO, registration number: CRD42019122295. We undertook searches of five databases, article references, and citations. Key authors in the field of health care VR were also contacted to identify additional papers. Articles were assessed for inclusion by two researchers independently. Data were extracted using standardized forms.

Results

Our search identified a total of 2,824 citations, following screening for duplicates and application of inclusion and exclusion criteria, five studies were included for analysis. Included studies were heterogeneous, with small sample sizes and mixed outcomes.

Discussion and Implications

We were unable to reach definitive conclusions over the use, acceptability, and effectiveness of IVR for dementia and mild cognitive impairment. Future studies should focus on ensuring their interventions are truly immersive, developing more robust controls and account for the rapid rate of obsolescence in digital technologies.
The use of linear mixed effects models to investigate local adaptation in marine fish subpopulations: case study, changing spawning times of common sole (Solea solea)
Authors: Fincham Jennifer I , Barry Jon
Published: September 2019

Populations along environmental gradients have the potential to adapt to their own local environments. It is important to understand these adaptations in fisheries stocks to fully inform fisheries management strategies. With this is mind, sea temperatures are an important cue in timing for many marine species, including sole in the North-East Atlantic Ocean. We used spawning data and modelled sea surface temperature (SST) data from sole subpopulations to examine the possibility of local adaptation of their spawning times to rising temperature. Climate window analysis was used, in a linear mixed model using mean spawning week and SST, to investigate statistically significant differences between subpopulations of sole. There was no evidence of local adaptation to changing temperatures for these subpopulations. This suggests that their spawning-time reaction to changing temperatures is currently due to their subpopulation’s mean plasticity. Using climate window analysis and modelled temperature data we have demonstrated a method of examining spawning changes in marine populations along a temperature gradient. Recruitment and spawning success are key elements of fisheries population models which contribute to fisheries management. Further understanding of the influence of temperature on recruitment will help inform future modelling.
Assessment of interactions between 205 breast cancer susceptibility loci and 13 established risk factors in relation to breast cancer risk, in the Breast Cancer Association Consortium
Authors: Kapoor Pooja Middha , Lindström Sara , Behrens Sabine , Wang Xiaoliang , Michailidou Kyriaki , Bolla Manjeet K , Wang Qin , Dennis Joe , Dunning Alison M , Pharoah Paul D P , Schmidt Marjanka K , Kraft Peter , García-Closas Montserrat , Easton Douglas F , Milne Roger L , Chang-Claude Jenny ,   on behalf of Breast Cancer Association Consortium
Published: September 2019

Background

Previous gene-environment interaction studies of breast cancer risk have provided sparse evidence of interactions. Using the largest available dataset to date, we performed a comprehensive assessment of potential effect modification of 205 common susceptibility variants by 13 established breast cancer risk factors, including replication of previously reported interactions.

Methods

Analyses were performed using 28 176 cases and 32 209 controls genotyped with iCOGS array and 44 109 cases and 48 145 controls genotyped using OncoArray from the Breast Cancer Association Consortium (BCAC). Gene-environment interactions were assessed using unconditional logistic regression and likelihood ratio tests for breast cancer risk overall and by estrogen-receptor (ER) status. Bayesian false discovery probability was used to assess the noteworthiness of the meta-analysed array-specific interactions.

Results

Noteworthy evidence of interaction at ≤1% prior probability was observed for three single nucleotide polymorphism (SNP)-risk factor pairs. SNP rs4442975 was associated with a greater reduction of risk of ER-positive breast cancer [odds ratio (OR)int = 0.85 (0.78-0.93), Pint = 2.8 x 10–4] and overall breast cancer [ORint = 0.85 (0.78-0.92), Pint = 7.4 x 10–5) in current users of estrogen-progesterone therapy compared with non-users. This finding was supported by replication using OncoArray data of the previously reported interaction between rs13387042 (r2 = 0.93 with rs4442975) and current estrogen-progesterone therapy for overall disease (Pint = 0.004). The two other interactions suggested stronger associations between SNP rs6596100 and ER-negative breast cancer with increasing parity and younger age at first birth.

Conclusions

Overall, our study does not suggest strong effect modification of common breast cancer susceptibility variants by established risk factors.
Molecular and genetic basis of azole antifungal resistance in the opportunistic pathogenic fungusCandida albicans
Authors: Nishimoto Andrew T , Sharma Cheshta , Rogers P David
Published: September 2019

Candida albicans is an opportunistic yeast and the major human fungal pathogen in the USA, as well as in many other regions of the world. Infections with C. albicans can range from superficial mucosal and dermatological infections to life-threatening infections of the bloodstream and vital organs. The azole antifungals remain an important mainstay treatment of candidiasis and therefore the investigation and understanding of the evolution, frequency and mechanisms of azole resistance are vital to improving treatment strategies against this organism. Here the organism C. albicans and the genetic changes and molecular bases underlying the currently known resistance mechanisms to the azole antifungal class are reviewed, including up-regulated expression of efflux pumps, changes in the expression and amino acid composition of the azole target Erg11 and alterations to the organism’s typical sterol biosynthesis pathways. Additionally, we update what is known about activating mutations in the zinc cluster transcription factor (ZCF) genes regulating many of these resistance mechanisms and review azole import as a potential contributor to azole resistance. Lastly, investigations of azole tolerance in C. albicans and its implicated clinical significance are reviewed.
Serum and peritoneal exudate concentrations after high doses of β-lactams in critically ill patients with severe intra-abdominal infections: an observational prospective study
Authors: Leon Lisa , Guerci Philippe , Pape Elise , Thilly Nathalie , Luc Amandine , Germain Adeline , Butin-Druoton Anne-Lise , Losser Marie-Reine , Birckener Julien , Scala-Bertola Julien , Novy Emmanuel
Published: September 2019

Background

Critically ill patients with severe intra-abdominal infections (IAIs) requiring surgery may undergo several pharmacokinetic (PK) alterations that can lead to β-lactam underdosage.

Objectives

To measure serum and peritoneal exudate concentrations of β-lactams after high doses and optimal administration schemes.

Methods

This observational prospective study included critically ill patients with suspicion of IAI who required surgery and a β-lactam antibiotic as empirical therapy. Serum and peritoneal exudate concentrations were measured during surgery and after a 24 h steady-state period. The PK/pharmacodynamic (PD) target was to obtain serum β-lactam concentrations of 100% fT>4×MIC based on a worst-case scenario (based on the EUCAST highest epidemiological cut-off values) before bacterial documentation (a priori) and redefined following determination of the MIC for the isolated bacteria (a posteriori). Registered with ClinicalTrials.gov (NCT03310606).

Results

Forty-eight patients were included with a median (IQR) age of 64 (53–74) years and a SAPS II of 40 (32–65). The main diagnosis was secondary nosocomial peritonitis. Piperacillin/tazobactam was the most administered β-lactam antibiotic (75%). The serum/peritoneal piperacillin/tazobactam ratio was 0.88 (0.64–0.97) after a 24 h steady-state period. Prior to bacterial documentation, 16 patients (33.3%) achieved the a priori PK/PD target. The identification of microorganisms was available for 34 patients (71%). Based on the MIC for isolated bacteria, 78% of the patients achieved the serum PK/PD target.

Conclusions

In severe IAIs, high doses of β-lactams ensured 100% fT>4×MIC in the serum for 78% of critically ill patients with severe IAIs within the first 24 h. In order to define optimal β-lactam dosing, the PK/PD target should take into account the tissue penetration and local ecology.