Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance of Pseudapanteles dignus (Hymenoptera: Braconidae), a Natural Enemy of Tuta absoluta (Lepidoptera: Gelechiidae) in Eggplant

Abstract Pseudapanteles dignus (Muesebeck; Hymenoptera: Braconidae) is an American endoparasitoid that attacks the South American tomato leafminer Tuta absoluta (Meyrick; Lepidoptera: Gelechiidae). The interaction between P. dignus and T. absoluta in tomato (Solanum lycopersicum L.; Solanales: Solanaceae) crops has demonstrated that this enemy exhibits some desirable ecological traits as an effective biological control agent of this pest. With the aim of extending the use of P. dignus to other solanaceous crops, laboratory experiments were carried out to assess some life history traits and the parasitism efficiency when parasitizing T. absoluta larvae fed on eggplant (Solanum melongena L.; Solanales: Solanaceae). Rearings and experiments were conducted at 25 ± 2°C, ≈70% RH, and 14:10 (L:D) h photoperiod, and T. absoluta was fed with eggplant. P. dignus developmental times of immature stages were lower (∼ 5 d) on S. melongena than on S. lycopersicum.The female did not exhibit a pre-reproductive period, and its oviposition period lasted longer (∼ 4 d) than that determined in tomato plants. Adult longevity was ca. 24 d for both sexes. Females produced ca. 61 cocoons during their lives and the maximum daily percentage of parasitism was 50% at the first day of adult emergence. Functional response of P. dignus on eggplant was density-independent of the host density offered, as in tomato plant, and the instantaneous attack rate (a′) was 0.24 attacked larvae/ available larvae, in 24 h. Our results indicate that although there are differences, P. dignus would have a similar performance in eggplant and tomato in terms of its efficacy in the control of T. absoluta.
Apelin: A putative novel predictive biomarker for bevacizumab response in colorectal cancer

Bevacizumab (bvz) is currently employed as an anti-angiogenic therapy across several cancer indications. Bvz response heterogeneity has been well documented, with only 10-15% of colorectal cancer (CRC) patients benefitting in general. For other patients, clinical efficacy is limited and side effects are significant. This reinforces the need for a robust predictive biomarker of response. To identify such a biomarker, we performed a DNA microarray-based transcriptional profiling screen with primary endothelial cells (ECs) isolated from normal and tumour colon tissues. Thirteen separate populations of tumour-associated ECs and 10 of normal ECs were isolated using fluorescence-activated cell sorting. We hypothesised that VEGF-induced genes were overexpressed in tumour ECs; these genes could relate to bvz response and serve as potential predictive biomarkers. Transcriptional profiling revealed a total of 2,610 differentially expressed genes when tumour and normal ECs were compared. To explore their relation to bvz response, the mRNA expression levels of top-ranked genes were examined using quantitative PCR in 30 independent tumour tissues from CRC patients that received bvz in the adjuvant setting. These analyses revealed that the expression of MMP12 and APLN mRNA was significantly higher in bvz non-responders compared to responders. At the protein level, high APLN expression was correlated with poor progression-free survival in bvz-treated patients. Thus, high APLN expression may represent a novel predictive biomarker for bvz unresponsiveness.
Clinical chorioamnionitis at term III: how well do clinical criteria perform in the identification of proven intra-amniotic infection?

Abstract Objective: The diagnosis of clinical chorioamnionitis is based on a combination of signs [fever, maternal or fetal tachycardia, foul-smelling amniotic fluid (AF), uterine tenderness and maternal leukocytosis]. Bacterial infections within the amniotic cavity are considered the most frequent cause of clinical chorioamnionitis and an indication for antibiotic administration to reduce maternal and neonatal morbidity. Recent studies show that only 54% of patients with the diagnosis of clinical chorioamnionitis at term have bacteria in the AF and evidence of intra-amniotic inflammation. The objective of this study was to examine the performance of the clinical criteria for the diagnosis of chorioamnionitis to identify patients with microbial-associated intra-amniotic inflammation (also termed intra-amniotic infection). Materials and methods: This retrospective cross-sectional study included 45 patients with the diagnosis of clinical chorioamnionitis at term, whose AF underwent analysis for: 1) the presence of microorganisms using both cultivation and molecular biologic techniques [polymerase chain reaction (PCR) with broad primers], and 2) interleukin (IL)-6 concentrations by enzyme-linked immunosorbent assay. The diagnostic performance (sensitivity, specificity, accuracy, and likelihood ratios) of each clinical sign and their combination to identify clinical chorioamnionitis were determined using microbial-associated intra-amniotic inflammation [presence of microorganisms in the AF using cultivation or molecular techniques and elevated AF IL-6 concentrations (≥2.6 ng/mL)] as the gold standard. Results: The accuracy of each clinical sign for the identification of microbial-associated intra-amniotic inflammation (intra-amniotic infection) ranged between 46.7% and 57.8%. The combination of fever with three or more clinical criteria did not substantially improve diagnostic accuracy. Conclusion: In the presence of a fever during labor at term, signs used to diagnose clinical chorioamnionitis do not accurately identify the patient with proven intra-amniotic infection (i.e., those with microorganisms detected by culture or molecular microbiologic techniques and an associated intra-amniotic inflammatory response).
Halophilic Microorganisms Are Responsible for the Rosy Discolouration of Saline Environments in Three Historical Buildings with Mural Paintings

A number of mural paintings and building materials from monuments located in central and south Europe are characterized by the presence of an intriguing rosy discolouration phenomenon. Although some similarities were observed among the bacterial and archaeal microbiota detected in these monuments, their origin and nature is still unknown. In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques. The bacterial communities were dominated by halophilic members of Actinobacteria, mainly of the genus Rubrobacter. Representatives of the Archaea were also detected with the predominating genera Halobacterium, Halococcus and Halalkalicoccus. Furthermore, halophilic bacterial strains, mainly of the phylum Firmicutes, could be retrieved from two monuments using special culture media. Inoculation of building materials (limestone and gypsum plaster) with selected isolates reproduced the unaesthetic rosy effect and biodeterioration in the laboratory.
Vasculogenic hydrogel enhances islet survival, engraftment, and function in leading extrahepatic sites

VEGF-delivering synthetic hydrogel improves islet survival and function in extrahepatic transplant sites over current clinical method. Islet transplantation is a promising alternative therapy for insulin-dependent patients, with the potential to eliminate life-threatening hypoglycemic episodes and secondary complications of long-term diabetes. However, widespread application of this therapy has been limited by inadequate graft function and longevity, in part due to the loss of up to 60% of the graft in the hostile intrahepatic transplant site. We report a proteolytically degradable synthetic hydrogel, functionalized with vasculogenic factors for localized delivery, engineered to deliver islet grafts to extrahepatic transplant sites via in situ gelation under physiological conditions. Hydrogels induced differences in vascularization and innate immune responses among subcutaneous, small bowel mesentery, and epididymal fat pad transplant sites with improved vascularization and reduced inflammation at the epididymal fat pad site. This biomaterial-based strategy improved the survival, engraftment, and function of a single pancreatic donor islet mass graft compared to the current clinical intraportal delivery technique. This biomaterial strategy has the potential to improve clinical outcomes in islet autotransplantation after pancreatectomy and reduce the burden on donor organ availability by maximizing graft survival in clinical islet transplantation for type 1 diabetes patients.
The Tol2kit: A multisite gateway‐based construction kit for Tol2 transposon transgenesis constructs

Transgenesis is an important tool for assessing gene function. In zebrafish, transgenesis has suffered from three problems: the labor of building complex expression constructs using conventional subcloning; low transgenesis efficiency, leading to mosaicism in transient transgenics and infrequent germline incorporation; and difficulty in identifying germline integrations unless using a fluorescent marker transgene. The Tol2kit system uses site‐specific recombination‐based cloning (multisite Gateway technology) to allow quick, modular assembly of [promoter]–[coding sequence]–[3′ tag] constructs in a Tol2 transposon backbone. It includes a destination vector with a cmlc2:EGFP (enhanced green fluorescent protein) transgenesis marker and a variety of widely useful entry clones, including hsp70 and beta‐actin promoters; cytoplasmic, nuclear, and membrane‐localized fluorescent proteins; and internal ribosome entry sequence–driven EGFP cassettes for bicistronic expression. The Tol2kit greatly facilitates zebrafish transgenesis, simplifies the sharing of clones, and enables large‐scale projects testing the functions of libraries of regulatory or coding sequences. Developmental Dynamics 236:3088–3099, 2007. © 2007 Wiley‐Liss, Inc.
Visual Attention during Spatial Language Comprehension

Spatial terms such as “above”, “in front of”, and “on the left of” are all essential for describing the location of one object relative to another object in everyday communication. Apprehending such spatial relations involves relating linguistic to object representations by means of attention. This requires at least one attentional shift, and models such as the Attentional Vector Sum (AVS) predict the direction of that attention shift, from the sausage to the box for spatial utterances such as “The box is above the sausage”. To the extent that this prediction generalizes to overt gaze shifts, a listener’s visual attention should shift from the sausage to the box. However, listeners tend to rapidly look at referents in their order of mention and even anticipate them based on linguistic cues, a behavior that predicts a converse attentional shift from the box to the sausage. Four eye-tracking experiments assessed the role of overt attention in spatial language comprehension by examining to which extent visual attention is guided by words in the utterance and to which extent it also shifts “against the grain” of the unfolding sentence. The outcome suggests that comprehenders’ visual attention is predominantly guided by their interpretation of the spatial description. Visual shifts against the grain occurred only when comprehenders had some extra time, and their absence did not affect comprehension accuracy. However, the timing of this reverse gaze shift on a trial correlated with that trial’s verification time. Thus, while the timing of these gaze shifts is subtly related to the verification time, their presence is not necessary for successful verification of spatial relations.
Phenological Adaptations in Ficus tikoua Exhibit Convergence with Unrelated Extra-Tropical Fig Trees

Flowering phenology is central to the ecology and evolution of most flowering plants. In highly-specific nursery pollination systems, such as that involving fig trees (Ficus species) and fig wasps (Agaonidae), any mismatch in timing has serious consequences because the plants must balance seed production with maintenance of their pollinator populations. Most fig trees are found in tropical or subtropical habitats, but the dioecious Chinese Ficus tikoua has a more northerly distribution. We monitored how its fruiting phenology has adapted in response to a highly seasonal environment. Male trees (where fig wasps reproduce) had one to three crops annually, whereas many seed-producing female trees produced only one fig crop. The timing of release of Ceratosolen fig wasps from male figs in late May and June was synchronized with the presence of receptive figs on female trees, at a time when there were few receptive figs on male trees, thereby ensuring seed set while allowing remnant pollinator populations to persist. F. tikoua phenology has converged with those of other (unrelated) northern Ficus species, but there are differences. Unlike F. carica in Europe, all F. tikoua male figs contain male flowers, and unlike F. pumila in China, but like F. carica, it is the second annual generation of adult wasps that pollinate female figs. The phenologies of all three temperate fig trees generate annual bottlenecks in the size of pollinator populations and for female F. tikoua also a shortage of fig wasps that results in many figs failing to be pollinated.
Phenotypic, Molecular and Symbiotic Characterization of the Rhizobial Symbionts of Desmanthus paspalaceus (Lindm.) Burkart That Grow in the Province of Santa Fe, Argentina

Desmanthus paspalaceus (Lindm.) Burkart belongs to the D. virgatus complex, subfamily Mimosoidae. The known potential as livestock fodder of several of these legumes prompted us to undertake a phenotypic, molecular, and symbiotic characterization of the D. paspalaceus symbionts in the Santa Fe province, Argentina. The rhizobia collected—containing isolates with different abiotic-stress tolerances—showed a remarkable genetic diversity by PCR fingerprinting, with 11 different amplification profiles present among 20 isolates. In selected isolates 16S-rDNA sequencing detected mesorhizobia (60%) and rhizobia (40%) within the collection, in contrast to the genus of the original inoculant strain CB3126—previously isolated from Leucaena leucocephala—that we typified here through its 16S rDNA as Sinorhizobium terangae. The results revealed the establishment by diverse bacterial genera -rhizobia, sinorhizobia, and mesorhizobia- of full N2-fixing symbiotic associations with D. paspalaceus. This diversity was paralleled by the presence of at least two different nodC allelic variants. The identical nodC alleles of the Mesorhizobia sp. 10.L. 4.2 and 10.L. 5.3 notably failed to group within any of the currently described rhizo-/brady-/azorhizobial nodC clades. Interestingly, the nodC from S. terangae CB3126 clustered close to homologs from common bean nodulating rhizobia, but not with the nodC from S. terangae WSM1721 that nodulates Acacia. No previous data were available on nod-gene phylogeny for Desmanthus symbionts. A field assay indicated that inoculation of D. paspalaceus with the local Rhizobium sp. 10L.11. 4 produced higher aerial-plant dry weights compared to S. teranga CB3126–inoculated plants. Neither the mesorhizobia 10.L. 4.2 or 10.L. 5.3 nor the rhizobium 10L.11. 4 induced root nodules in L. leucocephala or P. vulgaris. The results show that some of the local isolates have remarkable tolerances to several abiotic stresses including acidity, salt, and temperature; while exhibiting prominent N2 fixation; thus indicating suitability as candidates for inoculation of D. paspalaceus.
Is Antimicrobial Photodynamic Therapy Effective for Microbial Load Reduction in Peri‐implantitis Treatment? A Systematic Review and Meta‐Analysis

The systematic review and meta‐analysis were undertaken to evaluate the effectiveness of antimicrobial photodynamic therapy (aPDT) in the microbiological alteration beneficial to peri‐implantitis treatment. This study is registered with PROSPERO, number CRD42017064215. Bibliographic databases including Cochrane Library, Web of Science, Scopus and PubMed were searched from inception to 8 January 2017. The search strategy was assembled from the following MeSH Terms: “Photochemotherapy,” “Dental Implants” and “Peri‐Implantitis. ” Unspecific free‐text words and related terms were also included. The Cochrane Collaboration's tool was used to evaluate the risk of bias of included studies. The random‐effect model was chosen, and heterogeneity was evaluated using the I2 test. Three studies met the inclusion criteria. Meta‐analysis demonstrated an association between aPDT and reduction in viable bacteria counts for: Aggregatibacter actinomycetemcomitans (OR = 1.31; confidence interval = 1.13, 1.49; P < 0.00001), Porphyromonas gingivalis (OR = 4.08; confidence interval = 3.22, 4.94; P < 0.00001) and Prevotella intermedia (OR = 1.66; confidence interval = 1.06, 2.26; P < 0.00001). A aPDT appears to be effective in bacterial load reduction in peri‐implantitis and has a positive potential as an alternative therapy for peri‐implantitis.
The Effects of a Competitor on the Foraging Behaviour of the Shore Crab Carcinus maenas

Optimal Diet Theory suggests that individuals make foraging decisions that maximise net energy intake. Many studies provide qualitative support for this, but factors such as digestive constraints, learning, predation-risk and competition can influence foraging behaviour and lead to departures from quantitative predictions. We examined the effects of intraspecific competition within a classic model of optimal diet – the common shore crab, Carcinus maenas, feeding on the mussel, Mytilus edulis. Unexpectedly, we found that breaking time (Tb), eating time (Te), and handling time (Th) all decreased significantly in the presence of a conspecific. Reduced handling time in the presence of a competitor resulted in an increased rate of energy intake, raising the question of why crabs do not always feed in such a way. We suggest that the costs of decreased shell breaking time may be increased risk of claw damage and that crabs may be trading-off the potential loss of food to a competitor with the potential to damage their claw whilst breaking the shell more rapidly. It is well documented that prey-size selection by crabs is influenced by both the risk of claw damage and competition. However, our results are the first to demonstrate similar effects on prey handling times. We suggest that crabs maximise their long-term rate of energy intake at a scale far greater than individual foraging events and that in order to minimise claw damage, they typically break shells at a rate below their maximum. In the presence of a competitor, crabs appear to become more risk-prone and handle their food more rapidly, minimising the risk of kleptoparasitism.
Effects of GWAS-Associated Genetic Variants on lncRNAs within IBD and T1D Candidate Loci

Long non-coding RNAs are a new class of non-coding RNAs that are at the crosshairs in many human diseases such as cancers, cardiovascular disorders, inflammatory and autoimmune disease like Inflammatory Bowel Disease (IBD) and Type 1 Diabetes (T1D). Nearly 90% of the phenotype-associated single-nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) lie outside of the protein coding regions, and map to the non-coding intervals. However, the relationship between phenotype-associated loci and the non-coding regions including the long non-coding RNAs (lncRNAs) is poorly understood. Here, we systemically identified all annotated IBD and T1D loci-associated lncRNAs, and mapped nominally significant GWAS/ImmunoChip SNPs for IBD and T1D within these lncRNAs. Additionally, we identified tissue-specific cis-eQTLs, and strong linkage disequilibrium (LD) signals associated with these SNPs. We explored sequence and structure based attributes of these lncRNAs, and also predicted the structural effects of mapped SNPs within them. We also identified lncRNAs in IBD and T1D that are under recent positive selection. Our analysis identified putative lncRNA secondary structure-disruptive SNPs within and in close proximity (+/−5 kb flanking regions) of IBD and T1D loci-associated candidate genes, suggesting that these RNA conformation-altering polymorphisms might be associated with diseased-phenotype. Disruption of lncRNA secondary structure due to presence of GWAS SNPs provides valuable information that could be potentially useful for future structure-function studies on lncRNAs.
Allen Newell's Program of Research: The Video-Game Test

Newell (1973) argued that progress in psychology was slow because research focused on experiments trying to answer binary questions, such as serial versus parallel processing. In addition, not enough attention was paid to the strategies used by participants, and there was a lack of theories implemented as computer models offering sufficient precision for being tested rigorously. He proposed a three-headed research program: to develop computational models able to carry out the task they aimed to explain; to study one complex task in detail, such as chess; and to build computational models that can account for multiple tasks. This article assesses the extent to which the papers in this issue advance Newell's program. While half of the papers devote much attention to strategies, several papers still average across them, a capital sin according to Newell. The three courses of action he proposed were not popular in these papers: Only two papers used computational models, with no model being both able to carry out the task and to account for human data; there was no systematic analysis of a specific video game; and no paper proposed a computational model accounting for human data in several tasks. It is concluded that, while they use sophisticated methods of analysis and discuss interesting results, overall these papers contribute only little to Newell's program of research. In this respect, they reflect the current state of psychology and cognitive science. This is a shame, as Newell's ideas might help address the current crisis of lack of replication and fraud in psychology.
Variation at Genes Influencing Facial Morphology Are Not Associated with Developmental Imprecision in Human Faces

Facial asymmetries are commonly used as a proxy for human developmental imprecision resulting from inbreeding, and thus reduced genetic heterozygosity. Several environmental factors influence human facial asymmetry (e.g., health care, parasites), but the generalizability of findings on genetic stressors has been limited in humans by sample characteristics (island populations, endogamy) and indirect genetic assessment (inference from pedigrees). In a sample of 3215 adult humans from the Rotterdam Study, we therefore studied the relationship of facial asymmetry, estimated from nine mid-facial landmarks, with genetic variation at 102 single nucleotide polymorphism (SNP) loci recently associated with facial shape variation. We further tested whether the degree of individual heterozygosity is negatively correlated with facial asymmetry. An ANOVA tree regression did not identify any SNP relating to either fluctuating asymmetry or total asymmetry. In a general linear model, only age and sex—but neither heterozygosity nor any SNP previously reported to covary with facial shape—was significantly related to total or fluctuating asymmetry of the midface. Our study does not corroborate the common assumption in evolutionary and behavioral biology that morphological asymmetries reflect heterozygosity. Our results, however, may be affected by a relatively small degree of inbreeding, a relatively stable environment, and an advanced age in the Rotterdam sample. Further large-scale genetic studies, including gene expression studies, are necessary to validate the genetic and developmental origin of morphological asymmetries.