bluuebunny/crossref_metadata_2025 huggingface dataset:
Geographical Correlates of Abundance vs. Rarity in Some North American Winter Landbirds
Authors: Bock Carl E.
Published: September 2019

Using Christmas Bird Count (CBC) data, I compared range sizes and within-range abundances of 70 species of apodiform, piciform, and passerine landbirds whose ranges are 75% or more restricted in winter to the contiguous U.S. and southern Canada. Range size was computed as the number of occupied 5Â° latitude-longitude blocks. Three abundance measures were calculated: (1) mean birds counted/census hour across all occupied blocks, (2) maximum birds/hour in a single block, and (3) maximum birds/hour on a single CBC. Range size was positively but weakly correlated with each abundance measure, and the abundance measures were very strongly correlated with one another. Geography was a powerful predictor of the species' positions in a two-dimensional space difined by the axes of range size and average within-range abundance. Taxa that breed and winter at higher latitudes had larger total populations, and had significantly larger ranges and average local abundances. Species grouped by longitudinal areas of greatest local abundance had distinct range sizes but did not differ in average within-range abundance. Eastern species had larger ranges than comparably abundant western forms, probably because the eastern U.S. is characterized by relatively widespread habitat types. Results of this study suggest that a species' within-range abundance is influenced by the degree of its habitat generalization, whereas its range size will be larger if it is a habitat generalist or a specialist on widespread habitats. Because individual CBC's include many habitats, the same ecological attribute-habitat generalization-could cause species to be both widespread and abundant inside CBC circles. Carefully standardized within-habitat censuses will be required to determine whether or not these generalist species also dominate the individual habitats occupied by their more specialized and narrowly distributed relatives.
Reliability of Singing Bird Surveys: Changes in Observer Efficiency with Avian Density
Authors: Bart Jonathan , Schoultz James D.
Published: September 2019

Field trials in which paired observers were used and indoor simulations in which recorded bird songs were used indicated that, as the number of singing birds audible from a listening station increased from 1 to 4, the fraction of them recorded by observers declined by up to 50%. This reduction in efficiency violates one of the basic assumptions of any index-that the proportion of animals detected remains constant-and could cause surveyors who rely primarily on auditory cues to underestimate changes in population density by up to 25% for common species and 33% for abundant species. The change in efficiency, which is best regarded as measurement error, cannot be detected by a statistical examination of the data and thus may pass undetected in many field studies. It seems unlikely that any general procedure for "correcting" the error would be reliable. The results indicate that singing bird surveys of common species should be supplemented by other methods if accurate estimates of changes in density are needed. A general conclusion of the study is that whenever animals "compete" for a place in the survey, for example by filling up traps or suppressing one another's songs, then the index tends to underestimate a change in density. If efficiency increases with density, then the survey tends to overestimate a change in density. If the sign of the bias can be determined, the survey can be used to provide a minimum or maximum estimate of a change in density even if the magnitude of the bias cannot be estimated.
An Evaluation of Time-Budget Estimates of Daily Energy Expenditure in Birds
Authors: Weathers Wesley W. , Buttemer William A. , Hayworth Anita M. , Nagy Kenneth A.
Published: September 2019

We used the doubly-labeled water (DLW) technique to measure the daily energy expenditure (ḢTD) of aviary-housed Loggerhead Shrikes (Lanius ludovicianus). Simultaneously to our DLW measurements, we obtained a continuous 24-h record of the bird's time budget (TB) and assessed its thermal environment at 10-min intervals with an array of 23 meteorological sensors that measured the air temperature (Ta), operative temperature (Te), and wind speed (u) experienced by the bird. From the TB and meteorological data, we estimated the birds' ḢTV by several TB models that differed in the energy equivalents assigned to behaviors and in how thermoregulatory costs were calculated. Only a convection-adjusted, electrical-analog model provided a mean ḢTV estimate that was identical to the mean DLW value (106 kJ/day). Values of $\dot{H}_{TD}$ for individual birds calculated by this model ranged from -8.1 to +7.5% of the DLW values and were significantly correlated with the DLW values, indicating that this method accurately gauged the ḢTV of individual birds. Our analysis showed that this model's accuracy resulted from (1) using Te and u to calculate thermoregulatory costs through heat transfer theory, and (2) using measured energy equivalents for the various behavior categories. ḢTV estimates based on other commonly used TB models differed significantly from the DLW values, with mean errors ranging from -18 to +21%.
Territory Size Variations in Shrubsteppe Birds
Authors: Wiens John A. , Rotenberry John T. , Horne Beatrice Van
Published: September 2019

We recorded variations in sizes of breeding territories of Sage (Amphispiza belli) and Brewer's (Spizella breweri) sparrows at four locations in shrubsteppe habitats during 1976-1983. There was considerable variation in territory sizes of both species, and ANOVA tests indicated that site, plot within site, and year all contributed to this variation. Territory-size variations of Sage Sparrows were correlated with differences in several habitat features, while those of Brewer's Sparrows showed no relation to habitat variation. Territory sizes in both species varied inversely with breeding population densities, although in different ways. Our findings cast doubt on the meaning or value of "average" territory-size measures for a species as a whole.
Seasonal Changes in Feeding Success, Activity Patterns, and Weights of Nonbreeding Sanderlings (Calidris alba)
Authors: Maron J. L. , Myers J. P.
Published: September 2019

Seasonal changes in Sanderling (Calidris alba) feeding success, time budgets, and weights were followed throughout the nonbreeding season at Bodega Bay, California. Sanderlings spent more time roosting in fall than in winter, and in fall adults spent more time roosting than juveniles. Sanderling prey capture rates were high in fall and spring and declined through winter. Sanderling weights paralleled seasonal changes in feeding success and activity patterns: birds were heaviest in fall and spring and lightest in winter. These results reflect lowered food availability in winter and imply that birds may have difficulty balancing their energy budgets during part of the nonbreeding season.
Recognition of Parents' Voices by Young Cliff Swallows
Authors: Beecher Michael D. , Stoddard Philip K. , Loesche Patricia
Published: September 2019

Cliff Swallow (Hirundo pyrrhonota) chicks were played calls of parents and unrelated (control) adults at 9 and 18 days of age. Younger chicks showed no difference in the frequency of their antiphonal begging calls to parental vs. control calls. The older, near-fledging chicks, however, responded significantly more to parental calls than to control calls: 78% of their total antiphonal calls were in response to parental playback calls. In these older chicks, the degree of preference correlated with the measured acoustic differences between the parent and control calls. The results indicate that Cliff Swallow chicks are able to recognize their parents by voice before they leave the nest. Offspring recognition of parents is discussed as it relates to the evolution of parent-offspring recognition systems in general.
Parental Investment by the Northern Mockingbird: Male and Female Roles in Feeding Nestlings
Authors: Breitwisch Randall , Merritt Peter G. , Whitesides George H.
Published: September 2019

Analysis of 3,293 feeding trips to nestling Northern Mockingbirds (Mimus polyglottos) in the first 11 days of nestling life showed that males and females fed young at similar rates. Young were fed a mixed diet of animal prey and fruits, and males and females fed similar volumes of animal prey and of fruits. Females displayed a monotonic increase in feeding rate during nestling life but did not significantly increase load size. Males significantly increased both feeding rate and load size with age of nestlings, and their feeding rate peaked in the mid-nestling period, when young grow most rapidly. Males and females fed broods of two and three young at similar rates. There was a biased breeding-adult sex ratio in this population, with males outnumbering females. The unbalanced sex ratio may allow females to demand a high level of male parental care in feeding nestlings and in other behaviors included in parental investment.
Family Associations in Communally Roosting Black Vultures
Authors: Rabenold Patricia Parker
Published: September 2019

Observations of marked individuals in a partially marked population of Black Vultures (Coragyps atratus) show that immediate family members maintain close contact throughout the year. Associations between mates and between parents and offspring are primarily responsible for this. Mutual allopreening, feedings, and intercessions in fights occur almost exclusively within families. Adults known to breed within the study area (neighbors) associate more strongly than nonneighbors, although not as strongly as mates. Certain families associate preferentially with certain other families. Strength of interfamily associations is not related to distance between nest sites within the study area. I argue, therefore, that birds actively seek particular individuals as associates. Further knowledge of breeding dispersal of young of known parentage will provide clues to relatedness of highly associated neighbors. Strong associations among related individuals can help explain the use of avian communal roosts as information centers.
Reproductive Performance of Seabirds: The Importance of Population and Colony Size
Authors: Hunt George L. , Eppley Zoe A. , Schneider David C.
Published: September 2019

We compared reproductive performance of five species of seabirds at two colonies, St. George Island (2.5 million birds) and St. Paul Island (250,000 birds), in the southeastern Bering Sea. All species had lower chick growth rates at the larger colony, and the differences were statistically significant in four species. Fledge weights of Common Murres (Uria aalge) on St. George Island were 84-88% of those on St. Paul. Average fledge weights of Thick-billed Murres (Uria lomvia) on St. George were only 74% of those for chicks from St. Paul. We found no significant differences in clutch size or breeding success between populations breeding at the two colonies. For three species, Black-legged Kittiwakes (Rissa tridactyla), Common Murres, and Thick-billed Murres, we extended our analysis to include published data from other colonies. We examined breeding performance as a function of colony size, population size (suggestive of intraspecific competition), and "effective colony size," the sum of the populations of species with considerable dietary overlap (suggestive of interspecific competition for food). We found consistently negative relationships between population size and several measures of breeding performance (clutch size, growth rate, fledge weight, and breeding success). In addition to the lower breeding success at colonies that support large populations, chicks from these colonies may be subject to higher postfledging mortality because of fledging at lower weights.
Search Tactics of Insectivorous Birds Foraging in an Australian Eucalypt Forest
Authors: Holmes Richard T. , Recher Harry F.
Published: September 2019

The different ways birds searched for food in an Australian Eucalyptus forest led them to detect and capture different kinds of prey. Five major searching modes were identified among 23 common, mostly insectivorous bird species. These were distinguished largely by the rates, distances, and angles moved by birds while foraging and by their prey-capture behavior. Some bird species typically moved slowly, visually examining substrates at relatively long distances, and then took flight to capture prey (e.g. whistlers, flycatchers, muscicapid robins, cuckoos). Others moved at more rapid rates and either gleaned small prey from nearby substrates (e.g. thornbills, treecreepers) or flushed insects that were then pursued (e.g. fantails). Two species (Eastern Shrike-Tit, Falcunculus frontatus; White-eared Honeyeater, Meliphaga leucotis) were specialized substrate-restricted searchers, seeking invertebrate and carbohydrate foods among the exfoliating bark of Eucalyptus.

The search tactics of birds in this south temperate Australian forest were similar to those of birds in a north temperate forest in New Hampshire, USA, previously reported by Robinson and Holmes (1982). The differences in food-searching behavior between these phylogenetically distinct avifaunas (e.g. search flight and prey-attack flight lengths, hop/flight ratios, foraging rates) reflect the effects of unique foliage structures (e.g. spacing of branches, arrangements of leaves) and food resources at each site.

These findings support the hypothesis that habitat structure and food availability provide opportunities and constraints on how birds search for and capture food in forest habitats. These in turn are postulated to affect the success of particular bird species exploiting those habitats and thus influence bird community patterns.
Abundance and Habitat Selection of Two American Kestrel Subspecies in North-Central Florida
Authors: Bohall-Wood Petra , Collopy Michael W.
Published: September 2019

We censused American Kestrels (Falco sparverius) in the three vegetation communities representative of north-central Florida (pine flatwoods, sandhills, and agriculture/mixed hardwoods) along 24 16-km roadside transects. The winter kestrel population included resident F. s. paulus and migrant F. s. sparverius. Eighty-four percent of the 1,433 kestrels were sighted in winter, reflecting a significant influx of migrant F. s. sparverius, and were primarily females (65%). Significant (P < 0.05) sexual differences in winter habitat use were attributed to the large numbers of migrants. Males preferred closed habitats and smaller-sized open areas, and females preferred open habitats and larger open areas. Wintering kestrels were most abundant (P < 0.05) in the agriculture/mixed-hardwoods community (51%) and least abundant in the pine-flatwoods community (13%). Seventy-one percent of the 233 kestrels seen during summer were identified as F. s. paulus. Males and females were observed in approximately equal numbers and exhibited no differences in habitat preference. Falco s. paulus preferred the sandhill community (79%) to the agriculture/mixed hardwoods and pine flatwoods. Within the sandhill community, resident kestrels significantly increased their use of the pine/oak woodlands during summer.
Role of Sibling Aggression in Food Distribution to Nestling Cattle Egrets (Bubulcus Ibis)
Authors: Ploger Bonnie J. , Mock Douglas W.
Published: September 2019

Sibling aggression occurs in a wide variety of asynchronously hatching bird species. In some, fights among siblings lead inevitably to death, in which case the benefits of winning are clear. In species where sibling aggression is common but usually not fatal, the benefits gained by winning and the methods used to achieve them are less obvious. In a Texas colony of Cattle Egrets (Bubulcus ibis), sibling aggression was frequent but siblicide rare. Parents rarely interfered with fights. Last-hatched chicks lost more fights and received less food than their elder siblings. Fighting limited the losers' immediate access to food and contributed to the senior sib's ability to monopolize boluses. These results are consistent with the hypothesis that monopolizable food can act as both a proximate and ultimate cause of sibling aggression. The main effect of sibling aggression lay in depressing food supplies to last-hatched chicks. First- and second-hatched sibs accrued roughly equal feeding advantages.
Pairing Success of Kirtland's Warblers in Marginal vs. Suitable Habitat
Authors: Probst John R. , Hayes Jack P.
Published: September 2019

We compared pairing success of male Kirtland's Warblers (Dendroica kirtlandii) in different habitats to test the hypothesis that a lower proportion of males in marginal habitat are mated. Fewer than 60% of the males in marginal habitat were paired, but 95% of the males in suitable habitat were paired. We estimated the overall pairing success of the known breeding population at 85%. We could not estimate the number of females because the adult sex ratio is unknown, and an unknown proportion of Kirtland's Warblers are polygynous. The Kirtland's Warbler population was fairly constant from 1971 to 1983, despite markedly improved nest success resulting from cowbird control measures. If there are more males than females, or if many females fail to breed or must accept mated males or marginal habitat, population growth could be impeded. We combined reduced pairing success with an estimate of fledgling mortality, and revised the estimated number of fall immatures to between 369 and 471 birds-about 36% lower than the uncorrected estimate. Lower annual productivity of a static population implies higher annual survivorship of adults, yearlings, or both.
Increase of Parental Effort with Brood Size in a Nidifugous Bird
Authors: Schindler Martin , Lamprecht Jürg
Published: September 2019

Positive correlations of brood size with some parental activities [vigilance (in females), approaching young (in males and females), and attack (in males)] and a negative correlation of female feeding time with brood size were found in a sample of 23 semicaptive Bar-headed Goose (Anser indicus) families. Detailed examination of these correlations suggests that some components of parental care in geese represent "shared parental investment" (Lazarus and Inglis 1978, 1986). The benefits of parental care are divided among the offspring, so that in precocial birds, as in altricial birds, clutch size may be adapted to selection pressures that act after the young hatch.
Body and Organ Mass and Body Composition of Postbreeding Female Lesser Scaup
Authors: Austin Jane E. , Fredrickson Leigh H.
Published: September 2019

Changes in body and organ mass and body composition of postbreeding female Lesser Scaup (Aythya affinis) were investigated in the prairie-pothole region of southwestern Manitoba. Body mass was lowest during the wing molt and peaked during the migratory period. Most digestive organs gradually increased in mass through the postbreeding season. Lipid reserves remained relatively constant from the preflightless through the postflightless periods (x̄ = 43 g). The marked increase in lipids in the migratory period (x̄ = 183 g, P < 0.05) corresponded with premigratory hyperphagia. Time spent feeding explained 87% of the variation in lipid levels during the postbreeding season. Protein reserves declined with the onset of wing molt (P < 0.001) and increased during the postflightless period (P < 0.05). Breast muscle mass followed a similar pattern and was strongly correlated with molt intensity (r = 0.799, P < 0.001). Protein reserves, in particular the breast muscles, provide at least part of the protein required for feather production. Low body mass and lipid reserves during molt may not indicate energetic or nutritional stress but, alternatively, may be part of a postbreeding strategy to minimize energy demands and to reduce the length of the flightless period.
Cranial Kinesis in the Late Cretaceous Birds Hesperornis and Parahesperornis
Authors: Bühler Paul , Martin Larry D. , Witmer Lawrence M.
Published: September 2019

A recently discovered skull of the Cretaceous toothed diving bird Hesperornis permits evaluation of previous descriptions of the skull, analysis of cranial kinesis in hesperornithid birds, and discussion of the evolution of avian cranial kinesis. We found no evidence in hesperornithids for mesokinesis, a system that in lizards involves relative movement of the frontals and parietals. "Maxillokinesis," the fore-aft movements of the palato-maxillary arcade, was also rejected. Evidence for cranial kinesis in hesperornithid birds involves the presence of a streptostylic quadrate bone of virtually modern morphology, three types of flexion zones at the posterior end of the upper jaw, and a hiatus in the nasal-interorbital septum. Among the forms of kinesis found in modern birds, prokinesis, in which the upper jaw moves as a unit, was the dominant type of cranial kinesis in hesperornithids as indicated by the rigid construction of the upper jaw, the position of the holorhinal nostril, and the anteriorly truncate mesethmoid bone; rhynchokinesis and amphikinesis were not possible. Prokinesis is considered primitive for at least the group including Hesperornithiformes and later birds. Discovery of prokinesis in Hesperornis represents the first time all of the morphological correlated of prokinesis have been identified in a bird plesiomorphically lacking pterygoid segmentation.
Inter and Intraspecific Relationships between Egg Size and Clutch Size in Waterfowl
Authors: Rohwer Frank C.
Published: September 2019

Lack (1967, 1968a) proposed that clutch size of waterfowl and other birds with self-feeding young was limited by females' ability to produce eggs. Lack supported this egg-production hypothesis by showing a strong inverse relationship between egg size and clutch size within and among species of waterfowl. A reanalysis using updated data and more appropriate statistics failed to confirm Lack's results. Grouping all the waterfowl produced a weak (r2 = 0.13 inverse relationship between relative egg size and relative clutch size. This relationship was due mainly to a handful of ducks that nest on oceanic islands. Analyses by tribes showed that relative egg size and relative clutch size were inversely related in only 2 of the 8 major tribes of waterfowl. Finally, intraspecific analyses failed to reveal a trade-off between egg size and clutch size in Blue-winged Teal (Anas discors) and Northern Shovelers (A. clypeata). Similar intraspecific analyses for 12 other waterfowl have failed to show the predicted inverse relationship between egg size and clutch size. These results suggest that the widely accepted egg-production hypothesis may be considerably overemphasized.
The Scleral Ossicles of Opisthocomus and Their Phylogenetic Significance
Authors: Queiroz Kevin de , Good David A.
Published: September 2019

Dried scleral rings of Opisthocomus, Galliformes, Cuculiformes, and other birds were examined to determine the pattern of ossicle overlap in Opisthocomus and its bearing on the phylogenetic relationships of this taxon. Although Opisthocomus shares a derived number of 12 scleral ossicles with cuculid Cuculiformes, the pattern of ossicle overlap differs. Nevertheless, fewer modifications are required to derive the number and pattern of ossicles in Opisthocomus from the conditions in cuculid or musophagid Cuculiformes than from the conditions in any galliform. Our findings also indicate that the scleral rings of birds, unlike those of lizards, often do not conserve overlap relations between adjacent ossicles during phylogeny.
An Analysis of Function in the Formation Flight of Canada Geese
Authors: Badgerow John P.
Published: September 2019

I analyzed formations of Canada Geese (Branta canadensis) with a single, direct method of testing predictions from multiple hypotheses. The results support both energetic (aerodynamic) advantage and orientation communication through visual contact as functions of this complex behavior. Comparison of observed positioning patterns with criteria for optimal function suggests priority may be given to the maximization of energy savings within limits imposed by environmental and other constraints.
Activation of autophagy in early neonatal mice increases primordial follicle number and improves lifelong fertility†
Authors: Watanabe Ren , Sasaki Sho , Kimura Naoko
Published: September 2019

The number of stockpiled primordial follicles is thought to be responsible for the fate of female fertility and reproductive lifetime. We previously reported that starvation in nonsuckling early neonatal mice increases the number of primordial follicles with concomitant autophagy activation, suggesting that autophagy may accelerate the formation of primordial follicles. In this study, we attempted to upregulate the numbers of primordial follicles by administering an autophagy inducer and evaluated the progress of primordial follicle formation and their fertility during the life of the mice. To induce autophagy, mice were intraperitoneally injected with the Tat-beclin1 D-11 peptide (0.02 mg/g body weight) at 6–54 h or 60–84 h after birth. In animals that received Tat-beclin 1 D-11 by 54 h after birth, the primordial follicle numbers were significantly increased compared with the control group at 60 h. The ratio of expressed LC3-II/LC3-I proteins was also significantly greater. The numbers of littermates from pregnant females that had been treated with Tat-beclin 1 D-11 were maintained at remarkably greater levels until 10 months old. These results were supported by an abundance of primordial follicles at even 13–15 months old.
Protective effects of astaxanthin on lipopolysaccharide-induced inflammation in bovine endometrial epithelial cells†
Authors: Wan Fa-Chun , Zhang Chen , Jin Qing , Wei Chen , Zhao Hong-Bo , Zhang Xiang-Lun , You Wei , Liu Xiao-Mu , Liu Gui-Fen , Liu Yi-Fan , Tan Xiu-Wen
Published: September 2019

Astaxanthin (AST), a natural antioxidant carotenoid, has been shown to exert anti-inflammatory effects. However, to our knowledge, no study has specifically addressed the potential protective effects of AST against bovine endometritis. The purpose of this study was to examine whether treatment with AST could protect endometrial epithelial cells against lipopolysaccharide (LPS)-induced inflammatory injury. Treatment of bovine endometrial (BEND) epithelial cell line with AST reduced LPS-induced production of interleukin-6 and tumor necrosis factor-alpha, increased the cellular activity of superoxide dismutase and catalase, decreased the proportion of apoptotic cells, and promoted the production of insulin-like growth factor and epithelial growth factor. The effects of AST were mediated through the downregulation of B-cell lymphoma 2 (Bcl-2) associated X, apoptosis regulator (Bax), and cleaved caspase-3 and through the upregulation of Bcl-2. Moreover, AST significantly increased the expression of the tight junction proteins (TJP) claudin, cadherin-1, and TJP1, which play an essential role in the maintenance of host endometrial defense barrier against pathogen infection. Collectively, these results demonstrated that treatment with AST protected against oxidative stress, prevented cell apoptosis, promoted BEND cells viability, and increased the production of growth factors, in addition to activating the endometrial defense barrier. Therefore, AST is a promising therapeutic agent for the prevention and treatment of endometritis. This finding is of utmost importance in the present times when the excessive use of antibiotics has resulted in the development of antibiotic-resistant bacteria.
The first step towards personalized risk prediction for common epilepsies
Authors: Hansen Thomas F , Møller Rikke S
Published: September 2019

This scientific commentary refers to ‘Polygenic burden in focal and generalized epilepsies’, by Leu et al. (doi:10.1093/brain/awz292).
Past behavior and future judgements: seizing and freezing in response to cyber operations
Authors: Gomez Miguel Alberto
Published: September 2019

The use of cyber operations as a foreign policy instrument continues to stimulate academic interest towards interstate behavior in this domain. With continued investment in offensive cyber capabilities, there is an urgency to provide both academics and policy-makers with a better grasp of this phenomenon. While the past decade saw the growth of frameworks that highlight systemic and/or technological factors, this article investigates the role of pre-existing beliefs in the attribution of malicious cyber operations. Through survey experiments, it highlights the phenomenon of seizing and freezing with respect to attributive judgements in response to degradative cyber operations. With respect to theory, the results contribute to the emerging study of the cognitive–affective aspects of cyberspace. As for policy, the results illustrate the potential for biased judgements in response to incidents and reinforces the need to develop mechanisms that minimize its impact on state behavior.
Africa’s Voice in the Formation, Shaping and Redesign of International Investment Law
Authors: Mbengue Makane Moïse
Published: September 2019

Africa has often been presented as an ‘investment rules taker’, despite its longstanding contribution to the formation and shaping of the international investment regime. The present contribution seeks to analyze why Africa has been perceived as such and attempts to shed light on the active role that African countries have played since their independence in the development of the investment regime and also in the promotion of the ICSID system. The contribution also explores new avenues that are provided through the ‘Africanization’ of international investment law and their impact on the current redesign of the investment regime. It finally suggests options regarding the current negotiations of an Investment Protocol at the level of the African Union and ways to reinforce synergies between ICSID and the African Union.
Atomistic insight into the kinetic pathways for Watson–Crick to Hoogsteen transitions in DNA
Authors: Vreede Jocelyne , Pérez de Alba Ortíz Alberto , Bolhuis Peter G , Swenson David W H
Published: September 2019

DNA predominantly contains Watson–Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions between WC and HG may play a role in recognition and replication, but are difficult to investigate experimentally because they occur quickly, but only rarely. To gain insight into the mechanisms for this process, we performed transition path sampling simulations on a model nucleotide sequence in which an AT pair changes from WC to HG. This transition can occur in two ways, both starting with loss of hydrogen bonds in the base pair, followed by rotation around the glycosidic bond. In one route the adenine base converts from WC to HG geometry while remaining entirely within the double helix. The other route involves the adenine leaving the confines of the double helix and interacting with water. Our results indicate that this outside route is more probable. We used transition interface sampling to compute rate constants and relative free energies for the transitions between WC and HG. Our results agree with experiments, and provide highly detailed insights into the mechanisms of this important process.
VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium
Authors: Bagaev Dmitry V , Vroomans Renske M A , Samir Jerome , Stervbo Ulrik , Rius Cristina , Dolton Garry , Greenshields-Watson Alexander , Attaf Meriem , Egorov Evgeny S , Zvyagin Ivan V , Babel Nina , Cole David K , Godkin Andrew J , Sewell Andrew K , Kesmir Can , Chudakov Dmitriy M , Luciani Fabio , Shugay Mikhail
Published: September 2019

Here, we report an update of the VDJdb database with a substantial increase in the number of T-cell receptor (TCR) sequences and their cognate antigens. The update further provides a new database infrastructure featuring two additional analysis modes that facilitate database querying and real-world data analysis. The increased yield of TCR specificity identification methods and the overall increase in the number of studies in the field has allowed us to expand the database more than 5-fold. Furthermore, several new analysis methods are included. For example, batch annotation of TCR repertoire sequencing samples allows for annotating large datasets on-line. Using recently developed bioinformatic methods for TCR motif mining, we have built a reduced set of high-quality TCR motifs that can be used for both training TCR specificity predictors and matching against TCRs of interest. These additions enhance the versatility of the VDJdb in the task of exploring T-cell antigen specificities. The database is available at https://vdjdb.cdr3.net.
Aligned 3D porous polyurethane scaffolds for biological anisotropic tissue regeneration
Authors: Lin Weiwei , Lan Wanling , Wu Yingke , Zhao Daiguo , Wang Yanchao , He Xueling , Li Jiehua , Li Zhen , Luo Feng , Tan Hong , Fu Qiang
Published: September 2019

A green fabrication process (organic solvent-free) of artificial scaffolds is required in tissue engineering field. In this work, a series of aligned three-dimensional (3D) scaffolds are made from biodegradable waterborne polyurethane (PU) emulsion via directional freeze–drying method to ensure no organic byproducts. After optimizing the concentration of polymer in the emulsion and investigating different freezing temperatures, an aligned PUs scaffold (PU14) generated from 14 wt% polymer content and processed at −196°C was selected based on the desired oriented porous structure (pore size of 32.5 ± 9.3 μm, porosity of 92%) and balanced mechanical properties both in the horizontal direction (strength of 41.3 kPa, modulus of 72.3 kPa) and in the vertical direction (strength of 45.5 kPa, modulus of 139.3 kPa). The response of L929 cells and the regeneration of muscle tissue demonstrated that such pure material-based aligned 3D scaffold can facilitate the development of orientated cells and anisotropic tissue regeneration both in vitro and in vivo. Thus, these pure material-based scaffolds with ordered architecture have great potentials in tissue engineering for biological anisotropic tissue regeneration, such as muscle, nerve, spinal cord and so on.
P32 Kawasaki disease: learning points from 6 years of audit data from a large university teaching hospital
Authors: Patel Fahim , Sridhar Arani
Published: September 2019

Background

Kawasaki disease is the most common cause of acquired childhood heart disease in developed countries. If left untreated, 15 to 25% of children develop coronary artery aneurysms and more worryingly 2 to 3% will die from coronary vasculitis. Prompt recognition and management including referral to a cardiologist can ameliorate this. The clinical challenge however is the lack of any diagnostic tests and that many cases do not fit the typical diagnostic criteria.

Here we present the results from an original audit assessing our practice against RCPCH guidelines. We show findings from audit cycles spanning six years from Leicester’s children’s hospital. We also take one step further to analyse this data looking for trends in presentation and lab findings.

Methods

Original audit data was collected from cases between 2008-2012 and 2015-2017 (audit standards are shown in figure 1). The data generated from these audits was re-analysed to assess for trends in presentation and laboratory findings.

Results

In six years we saw 41 cases: 23 were of atypical presentation and 18 were typical (figure 2); 27 patients were male and 14 were female. The age range was 1 month to 13 years. All patients received IVIG, aspirin and were referred to cardiology. No patients required biological therapies. Cardiological events: Data incomplete – patients disseminated across several tertiary units; acutely - 6 patients had a borderline/abnormal echocardiogram; long-term - 1 patient has persistent but resolving coronary artery aneurysms.

Mortalities

A 4-month old in 2008 died as a result of untreated atypical Kawasaki disease. This patient was diagnosed only at autopsy.

Conclusion

Over the 2 audit periods we noted a higher than expected caseload of atypical KD. At presentation: 88% had no desquamation, 30% had only mildly raised CRP, and 2% did not have fever for more than 5 days.

Conflicts of Interest

The authors declare no conflicts of interest.
P53 Paediatric non-infectious dacryoadenitis: a single-centre experience
Authors: Silva-Dinis Joana , Solebo Ameenat Lola , Abou-Rayyah Yassir , Compeyrot-Lacassagne Sandrine
Published: September 2019

Background

Dacryoadenitis is an inflammatory enlargement of the lacrimal gland and can be idiopathic or associated with infections, malignant or inflammatory diseases like Sjögren’s disease (SSj) or granulomatosis with polyangiitis (GPA). It remains the most common orbital inflammatory condition in children.

This study purposes to describe a paediatric cohort of non-infectious dacryoadenitis.

Methods

Identification of children who underwent lacrimal gland biopsy at our centre between 2000 and 2018 was done by searching the database using two key-words: “lacrimal” and “dacryoadenitis”. Patients with infectious or malignant dacryoadenitis were excluded. Medical notes were reviewed to collect data.

Results

Twenty-six patients underwent lacrimal gland biopsy at our centre between 2000 and 2018 and had inflammatory dacryoadenitis. 17 patients (65.4%) had non-specific chronic inflammation (NSCI) and 9 patients (34.6%) had an inflammatory systemic condition (Table 1). P53 Table 1Patients’ characteristics.NSCIGPASarcoidosisSSjogrenIgG4Number of patients17 (65.4%)4 (15.4%)3 (11.5%)1 (3.9%)1 (3.9%)Female, n (%)6 (35.3%)4 (100%)3 (100%)1 (100%)1 (100%)Median age (Y) (IQ)10.5 (4.9- 14.4)9.72 (8.7- 13.0)13.2 (11.45- 15.7)11.911.2Lacrimal gland involvementUnilateral13 (74.5%)3 (75.0%)2 (66.7%)00Bilateral4 (23.5%)1 (25.0%)1 (33.3%)1 (100%)1 (100%)Orbital symptomsPtosis4 (23.5%)1 (25.0%)000Erythema3 (17.5%)1 (25.0%)1 (33.3%)00Pain2 (11.8%)1 (25.0%)000Extra-orbital involvementExocrine glands001 (33.3%)00ENT03 (75.0%)000Renal1 (14.3%)2 (50.0%)01 (100%)1 (100%)Pulmonary1 (14.3%)1 (25.0%)1 (33.3%)01 (100%)Myositis1 (14.3%)0000Arthralgia1 (14.3%)01 (33.3%)00Thyroiditis1 (14.3%)0000CNS0001 (100%)0Lymphadenopaties00001 (100%)

4/13 children tested had raised ACE (2 sarcoidosis and 2 NSCI). 7/17 had raised amylase (2 sarcoidosis,1 SSj, 4 NSCI). 3/16 had raised IgG (IgG4 disease, GPA and NSCI). ANA was positive in 4/19 patients (NSCI, GPA, Sarcoidose, SSj) and ANCA was positive in 4/19 patients (GPA).

Thirteen patients received steroids (oral or IV) and elevan received DMARDS (MMF, methotrexate, azathioprine and hydroxychloroquine). Four patients received biologic (rituximab, adalimumab or infliximab). Six patients underwent orbitotomy. Patients still on follow-up had good response to treatment.

One patient with NSCI presented with dacryoadenitis and later developed auto-immune thyroiditis and polymyositis, with positive ANA and anti-SRP antibodies. He was treated with steroids, methotrexate, MMF and IVIG.

Conclusion

Paediatric rheumatic inflammatory disorders have a diverse presentation and dacryoadenitis may be the initial manifestation. Biopsy is mandatory to exclude infection and malignancy. A full diagnostic workup is essential, especially if patients have positive ANA or ANCA.

Conflicts of Interest

The authors declare no conflicts of interest.
HpaP Sequesters HrpJ, an Essential Component of Ralstonia solanacearum Virulence That Triggers Necrosis in Arabidopsis
Authors: Lonjon Fabien , Rengel David , Roux Fabrice , Henry Céline , Turner Marie , Le Ru Aurélie , Razavi Narjes , Sabbagh Cyrus Raja Rubenstein , Genin Stéphane , Vailleau Fabienne
Published: September 2019

The Gram-negative bacterium Ralstonia solanacearum, the causal agent of bacterial wilt, is a worldwide major crop pathogen whose virulence strongly relies on a type III secretion system (T3SS). This extracellular apparatus allows the translocation of proteins, called type III effectors (T3Es), directly into the host cells. To date, very few data are available in plant-pathogenic bacteria concerning the role played by type III secretion (T3S) regulators at the posttranslational level. We have demonstrated that HpaP, a putative T3S substrate specificity switch protein of R. solanacearum, controls T3E secretion. To better understand the role of HpaP on T3S control, we analyzed the secretomes of the GMI1000 wild-type strain as well as the hpaP mutant using a mass spectrometry experiment (liquid chromatography tandem mass spectrometry). The secretomes of both strains appeared to be very similar and highlighted the modulation of the secretion of few type III substrates. Interestingly, only one type III-associated protein, HrpJ, was identified as specifically secreted by the hpaP mutant. HrpJ appeared to be an essential component of the T3SS, essential for T3S and pathogenicity. We further showed that HrpJ is specifically translocated in planta by the hpaP mutant and that HrpJ can physically interact with HpaP. Moreover, confocal microscopy experiments demonstrated a cytoplasmic localization for HrpJ once in planta. When injected into Arabidopsis thaliana leaves, HrpJ is able to trigger a necrosis on 16 natural accessions. A genome-wide association mapping revealed a major association peak with 12 highly significant single-nucleotide polymorphisms located on a plant acyl-transferase.
Stimulatory Effects of Boscalid on Virulence of Sclerotinia sclerotiorum Indicate Hormesis May Be Masked by Inhibitions
Authors: Hu Simin , Xu Qianru , Zhang Yuchao , Zhu Fuxing
Published: September 2019

Hormetic effects of fungicides on phytopathogens are of great importance for proper application of fungicides. The aim of the present study was to investigate the stimulatory effects of the fungicide boscalid on mycelial growth and virulence of the devastating plant pathogen Sclerotinia sclerotiorum. Boscalid in potato dextrose agar (PDA) at a dosage range from 0.0005 to 0.002 μg/ml exerted statistically significant (P ≤ 0.015) stimulations on mycelial growth of S. sclerotiorum, and the maximum stimulation magnitudes were 5.55 ± 0.73% (mean ± SD) for the four isolates tested. Boscalid in PDA at 0.02 μg/ml inhibited mycelial growth of isolates HLJ3H and HLJ4H by 15.0 and 8.9%, respectively. However, after the growth-inhibited mycelia were inoculated on rapeseed leaves, isolates HLJ3H and HLJ4H exhibited virulence stimulations of 8.7 and 17.8%, respectively, indicating that hormesis may be masked by inhibitions. Boscalid sprayed at 0.0001 to 0.1 μg/ml on detached rapeseed leaves had significant (P ≤ 0.041) stimulations on virulence of S. sclerotiorum, and the maximum stimulation magnitudes were 17.90 ± 5.94% (mean ± SD) for the four isolates tested. Experiments on 12 isolates with different levels of virulence showed there was a negative correlation (R = –0.663, P = 0.019) between the maximum virulence stimulation magnitude and virulence of S. sclerotiorum in the absence of fungicide. Boscalid at stimulatory concentrations had no significant effect on the expression levels of three virulence-associated genes that encode cutinase (SsCut), polygalacturonase (SsPG1), and oxaloacetate acetylhydrolase (SsOah1). The molecular mechanisms for hormetic effects of boscalid on S. sclerotiorum remain to be studied in the future.
Does the Duration of Cervical Radicular Symptoms Impact Outcomes After Anterior Cervical Discectomy and Fusion?
Authors: Basques Bryce A. , Ahn Junyoung , Markowitz Jonathan , Harada Garrett , Louie Philip K. , Mormol Jeremy , Varthi Arya , Goldberg Edward J. , An Howard S.
Published: September 2019

Study Design:

Retrospective cohort study.

Objective:

To compare clinical outcomes after anterior cervical discectomy and fusion (ACDF) based on preoperative duration of radiculopathy symptoms.

Summary of Background Data:

There is no clear indication of when outcomes after ACDF become less effective in the setting of acute versus chronic symptoms from cervical nerve root compression.

Materials and Methods:

A retrospective cohort study of consecutive patients who underwent an ACDF between 2008 and 2015 for radiculopathy was performed. Patients were divided into 3 groups: radicular symptoms lasting for <6 months, symptoms lasting for 6–12 months, and those with symptoms for ≥12 months. Neck Disability Index (NDI) and Visual Analog Scale (VAS) scores for both the neck and arms were obtained at preoperative and final postoperative visits. Radiographs were assessed for adjacent segment degeneration, fusion, and subsidence. Bivariate and multivariate regressions were subsequently used to compare outcomes between groups.

Results:

A total of 379 patients were included. Patients with symptoms lasting for 6–12 months and those with symptoms lasting for ≥12 months had worse preoperative VAS neck pain compared with patients with symptoms lasting for < 6 months (P=0.000 and P=0.004, respectively). Patients with symptoms lasting for ≥12 months had worse baseline functional status compared with patients with symptoms lasting for <6 months (P=0.009). At final follow-up, there were no significant differences in VAS neck, VAS arm, or NDI between symptom duration groups. However, differences in outcomes were noted when considering the type of preoperative symptom. Patients with pain symptoms of ≥12 months had worse preoperative VAS neck (P=0.001), VAS arm (P=0.008), and NDI (P<0.001) and had significantly worse final VAS arm (P=0.019) and NDI (P=0.016) compared with patients with preoperative pain symptoms lasting for <6 months. The overall reoperation rate was 4.5%. Fusion was achieved in 97.6% of the patients, and subsidence was observed in 5.5%. There were no significant differences in the risk of adjacent segment degeneration, reoperations, fusion rates, or subsidence rates based on preoperative symptom duration.

Conclusions:

Despite worse preoperative neck pain and functional status in patients with preoperative duration of symptoms >6 months, there were no differences in final clinical outcomes across groups.
Pathologic Response to Primary Systemic Therapy With FOLFIRINOX in Patients With Resectable Pancreatic Cancer
Authors: Polish Ariel , Joseph Nora E. , Marsh Robert de W.
Published: September 2019

Background:

Primary systemic therapy in resectable pancreatic cancer is currently under investigation. FOLFIRINOX has been shown to be effective in both the adjuvant and metastatic settings and is increasingly being used on and off study in the neoadjuvant setting. The objective pathologic response elicited by this regimen in truly resectable disease has not as yet been widely reported.

Methods:

This analysis focuses on 14 patients with resectable pancreatic cancer who were treated in a pilot study of primary systemic therapy, using 4 cycles of neoadjuvant FOLFIRINOX before surgery. A dedicated pancreatic pathologist reviewed all of the subsequent surgical specimens to assess the degree of tumor regression elicited by this approach, according to the scoring system proposed by Evans.

Results:

Four patients (28.6%) had Evans grade I, 4 (28.6%) Evans grade IIa, 2 (14.2%) Evans grade IIb, and 4 (28.6%) Evans grade III response to the primary systemic therapy. There were no Evans grade IV responses.

Conclusions:

The results are intriguing with 28% of the specimens showing destruction of <10% of tumor cells, and only 28% achieving >90% destruction of tumor cells. The significant variation in response once again confirms the known heterogeneity in the biology of this cancer and clearly FOLFIRINOX is not equally effective in all patients. Future studies evaluating primary systemic therapy in pancreatic cancer should examine the optimal duration of therapy before surgery and should include a standardized pathologic grading scheme to better enable comparison of results.