Miracle-dz/UniFAR-FTUs huggingface dataset:
Medicago truncatula SOC1 Genes Are Up-regulated by Environmental Cues That Promote Flowering

Like Arabidopsis thaliana, the flowering of the legume Medicago truncatula is promoted by long day (LD) photoperiod and vernalization. However, there are differences in the molecular mechanisms involved, with orthologs of two key Arabidopsis thaliana regulators, FLOWERING LOCUS C (FLC) and CONSTANS (CO), being absent or not having a role in flowering time function in Medicago. In Arabidopsis, the MADS-box transcription factor gene, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (AtSOC1), plays a key role in integrating the photoperiodic and vernalization pathways. In this study, we set out to investigate whether the Medicago SOC1 genes play a role in regulating flowering time. Three Medicago SOC1 genes were identified and characterized (MtSOC1a–MtSOC1c). All three MtSOC1 genes, when heterologously expressed, were able to promote earlier flowering of the late-flowering Arabidopsis soc1-2 mutant. The three MtSOC1 genes have different patterns of expression. However, consistent with a potential role in flowering time regulation, all three MtSOC1 genes are expressed in the shoot apex and are up-regulated in the shoot apex of plants in response to LD photoperiods and vernalization. The up-regulation of MtSOC1 genes was reduced in Medicago fta1-1 mutants, indicating that they are downstream of MtFTa1. Insertion mutant alleles of Medicago soc1b do not flower late, suggestive of functional redundancy among Medicago SOC1 genes in promoting flowering.
Immunohistochemical Analysis of nm23/NDP Kinase Expression in Human Lung Adenocarcinoma: Association with Tumor Progression in Clara Cell Type

Levels of nm23-H1/nucleoside diphosphate kinase (NDP kinase) expression have been reported to correlate inversely with metastatic potential in some tumors but not in others. Whether or not nm23 gene product is associated with metastatic potential in lung cancer is not clear as yet. We therefore immunohistochemically examined the expression of nm23 gene products in primary lung adenocarcinomas according to cytologic subtypes in order to clarify the association of its expression with the clinical features of the disease. Seventy-two (64.9%) of the 111 lung adenocarcinomas were positive for nm23 protein. In lung adenocarcinoma of Clara cell type, high levels of nm23 expression were associated with advanced pathologic stage, positive lymph node status, and poorer prognosis (P < 0.05). However, no correlation with clinical outcome was observed in other cell types. Our data suggest that higher levels of nm23 expression are associated with tumor progression in lung adenocarcinoma of Clara cell type.
OpenNetVM: A Platform for High Performance Network Service Chains

Network middleboxes are growing in number and diversity. Middleboxes have been deployed widely to complement the basic end-to-end functionality provided by the Internet Protocol suite that depends only on the minimal functionality of a best-effort network layer. The move from purpose-built hardware middleboxes to software appliances running in virtual machines provides much needed deployment flexibility, but significant challenges remain. Just as Software Defined Networking (SDN) research and product development was greatly accelerated with the release of several open source SDN platforms, we believe that Network Function Virtualization (NFV) research can see similar growth with the development of a flexible platform that enables high performance NFV prototypes. Towards this end we have been building OpenNetVM, an efficient packet processing framework that greatly simplifies the development of network functions, as well as research into their management and optimization. OpenNetVM runs network functions in lightweight Docker containers, enabling fast startup and reducing memory overheads. The OpenNetVM platform manager provides load balancing, flexible flow management, and service name abstractions. OpenNetVM efficiently routes packets through dynamically created service chains, achieving throughputs of 10 Gbps even when traversing a chain of 6 NFs. In this paper we describe our architecture and evaluate its performance compared to existing NFV platforms.
A controlled evaluation of family behavior therapy in concurrent child neglect and drug abuse.

OBJECTIVE Approximately 50% of child protective service (CPS) referrals abuse drugs; yet, existing treatment studies in this population have been limited to case examinations. Therefore, a family-based behavioral therapy was evaluated in mothers referred from CPS for child neglect and drug abuse utilizing a controlled experimental design. METHOD Seventy-two mothers evidencing drug abuse or dependence and child neglect were randomly assigned to family behavior therapy (FBT) or treatment as usual (TAU). Participants were assessed at baseline, 6 months, and 10 months postrandomization. RESULTS As hypothesized, intent-to-treat repeated measures analyses revealed mothers referred for child neglect not due to their children being exposed to illicit drugs demonstrated better outcomes in child maltreatment potential from baseline to 6- and 10-month postrandomization assessments when assigned to FBT, as compared with TAU mothers and FBT mothers who were referred due to child drug exposure. Similar results occurred for hard drug use from baseline to 6 and 10 months postrandomization. However, TAU mothers referred due to child drug exposure were also found to decrease their hard drug use more than TAU mothers of non-drug-exposed children and FBT mothers of drug-exposed children at 6 and 10 months postrandomization. Although effect sizes for mothers assigned to FBT were slightly larger for marijuana use than TAU (medium vs. large), these differences were not statistically significant. Specific to secondary outcomes, mothers in FBT, relative to TAU, increased time employed from baseline to 6 and 10 months postrandomization. Mothers in FBT, compared to TAU, also decreased HIV risk from baseline to 6 months postrandomization. There were no differences in outcome between FBT and TAU for number of days children were in CPS custody and alcohol intoxication, although FBT mothers demonstrated marginal decreases (p = .058) in incarceration from baseline to 6 months postrandomization relative to TAU mothers. CONCLUSION Family-based behavioral treatment programs offer promise in mothers who have been reported to CPS for concurrent substance abuse and child neglect of their children. However, continued intervention development in this population is very much needed.
Reflections on the Pre-Musical Moment

Patients in hospitals frequently have little choice about attending music therapy sessions. This, in addition to the novelty of music therapy as a treatment, may make both patient and therapist uncomfortable. The patient is unsure as to what to expect, and the music therapist uncertain as to how much to say—or leave unsaid. This article draws on the author's experience as a music therapist in a small adult psychiatric hospital. It is an attempt at examining the pre-musical moment at the time when both the patient and the music therapist are engaged in sharing their expectations and anxieties, and in negotiating a resolution before the musical-therapeutic process can begin.
Chitosan Induces Apoptosis via Caspase‐3 Activation in Bladder Tumor Cells

Recently, because of its low toxicity and biological effects, chitosan has been widely used in the medical and pharmaceutical fields, e.g., for nasal or oral delivery of peptide or polar drug delivery. Here, we report a growth‐inhibitory effect of chitosan on tumor cells. The growth inhibition was examined by WST‐1 colorimetric assay and cell counting. We also observed DNA fragmentation, which is characteristic of apoptosis, and elevated caspase‐3‐like activity in chitosan‐treated cancer cells. The findings suggest that chitosan may have potential value in cancer therapy.
Detection of Three Genetic Polymorphisms in the 5′‐Flanking Region and Intron 1 of Human CYP1A2 in the Japanese Population

Interindividual variability of the activity of CYP1A2 may be expected to affect cancer susceptibility, since the enzyme is capable of activating several carcinogens. In the present study, we found three new polymorphisms in the 5′‐flanking region (CYP1A2/B) and intron 1 (CYP1A2/C and CYP1A2/D) of CYP1A2 in Japanese by using polymerase chain reaction‐single strand conformation polymorphism. We developed methods to detect these polymorphisms by polymerase chain reaction‐restriction fragment length polymorphism and performed a population study (159 subjects) to estimate the frequencies of the alleles. The frequencies of the CYP1A2/A (adenine), CYP1A2/B (thymine‐deleted), CYP1A2/C (guanine) and CYP1A2/D (adenine) variants were 21.1, 42.0, 8.2 and 61.3%, respectively. The results of family study supported the idea that these CYP1A2 genotypes are inherited with an autosomal codominant transmission.
Activating learned exemplars in children impairs memory for related exemplars in visual long-term memory

A popular educational method when teaching children new information is encouraging children to activate previously learned information held in long-term memory. A potential downside of this practice is the considerable evidence that there are negative consequences of accessing long-term memory representations. Specifically, it has been shown that accessing information in long-term memory can actually impair related memories. This impairment has classically been demonstrated with verbal material (i.e., retrieval-induced forgetting) and more recently with visual material in adults (i.e., recognition-induced forgetting). The goal of the present study was to examine whether recognition-induced forgetting exists in visual long-term memory for children aged 6–10 years old, the age at which retrieval-induced forgetting appears to emerge. To this end, we presented children with an abbreviated, age-appropriate recognition-induced forgetting paradigm. If children suffer recognition-induced forgetting, practicing a subset of objects from a category of objects will impair memory for the other, non-practiced objects from the same category. The results showed that children across all ages showed impaired memory for non-practiced objects from practiced categories and no benefit from recognition practice for the younger children. These findings show that children's visual long-term memory is vulnerable to recognition-induced forgetting and does not appear to benefit from recognition practice.
Person Licensing and the Derivation of PCC Effects

1. The Person Case Constraint The Person-Case Constraint (PCC) is a universal condition on the distribution of marked person features in certain configurations. First thoroughly investigated by Bonet (1991), she concluded that in combinations of a direct and indirect object, both of which are phonologically weak, the direct object may not be 1 or 2 person (Bonet 1991:177). The following French example has analogues in all the Romance languages, as well as Greek, Czech, Swiss German, Basque, Georgian etc.:
On the trophic regimes of the Mediterranean Sea: a satellite analysis

Abstract. The ten years of the SeaWiFS satellite surface chlorophyll concentration observations, presently available, were used to characterize the biogeography of the Mediterranean Sea and the seasonal cycle of the surface biomass in different areas of the basin. The K-means cluster analysis was applied on the satellite time-series of chlorophyll concentration. The resulting coherent patterns were then explained on the basis of the present knowledge of the basin's functioning. Winter biomass enhancements were shown to occur in most of the basin and last for 2–3 months depending on the region. Classical spring bloom regimes were also observed, regularly in the North Western Mediterranean, and intermittently in four other specific areas. The geographical correspondence between specific clusters and regions showing high values of mean chlorophyll concentration indicates that, at least in the Mediterranean Sea, accumulations of phytoplankton are observed only where specific temporal trends are present.
Spontaneous renal adenocarcinoma in a Syrian hamster (Mesocricetus auratus ): frequency, morphological and immunohistochemical findings

A spontaneous adenocarcinoma occurred in one (0.22%) adult male Syrian hamster out of 443 necropsied from a breeding animal house of the state of Rio de Janeiro, Brazil. Gross inspection showed that the renal neoplasm consisted of a unilateral single white nodule of hard consistency located in the cortex, measuring 5 mm in diameter. Microscopically, the renal epithelial cells were markedly pleomorphic and presented an abundant granular eosinophilic cytoplasm. Cells were cuboidal and mainly formed trabeculae of various widths without a lumen and also formed solid areas. There were necrotic areas and three mitotic figures per 30 high-power fields. No intravascular invasion or metastasis was observed. Positive expression of vimentin and negative expression of cytokeratin 7, pan-cytokeratin and CD10 were observed in the tumor. The histopathology and immunohistochemical profile of the renal tumor suggested the diagnosis of the eosinophilic variant of adenocarcinoma, which was reported for the first time in this species.
Attenuating effects of ecosystem management on coral reefs

Local management improves coral reef’s capacity to recover from disturbances, but the signal attenuates unless properly measured. Managing diverse ecosystems is challenging because structuring drivers are often processes having diffuse impacts that attenuate from the people who were “managed” to the expected ecosystem-wide outcome. Coral reef fishes targeted for management only indirectly link to the ecosystem’s foundation (reef corals). Three successively weakening interaction tiers separate management of fishing from coral abundance. We studied 12 islands along the 700-km eastern Caribbean archipelago, comparing fished and unfished coral reefs. Fishing reduced biomass of carnivorous (snappers and groupers) and herbivorous (parrotfish and surgeonfish) fishes. We document attenuating but important effects of managing fishing, which explained 37% of variance in parrotfish abundance, 20% of variance in harmful algal abundance, and 17% of variance in juvenile coral abundance. The explained variance increased when we quantified herbivory using area-specific bite rates. Local fisheries management resulted in a 62% increase in the archipelago’s juvenile coral density, improving the ecosystem’s recovery potential from major disturbances.
The Impact of Social Media for Emergency Services: A Case Study with the Fire Department Frankfurt

The use of social media is not only part of everyday life but also of crises and emergencies. Many studies focus on the concrete use of social media during a specific emergency, but the prevalence of social media, data access and published research studies allows the examination in a broader and more integrated manner. This work-inprogress paper presents the results of a case study with the Fire Department Frankfurt, which is one of the biggest and most modern fire departments in Germany. The findings relate to social media technologies, organizational structure and roles, information validation, staff skills and resources, and the importance of volunteer communities. In the next step, the results will be integrated into the frame of a comparative case study with the overall aim of examining the impact of social media on how emergency services respond and react in an emergency.
A machine learning based framework to identify and classify long terminal repeat retrotransposons

Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. Accurate identification and classification of TEs present in a genome is an important step towards understanding their effects on genes and their role in genome evolution. We introduce TE-Learner, a framework based on machine learning that automatically identifies TEs in a given genome and assigns a classification to them. We present an implementation of our framework towards LTR retrotransposons, a particular type of TEs characterized by having long terminal repeats (LTRs) at their boundaries. We evaluate the predictive performance of our framework on the well-annotated genomes of Drosophila melanogaster and Arabidopsis thaliana and we compare our results for three LTR retrotransposon superfamilies with the results of three widely used methods for TE identification or classification: RepeatMasker, Censor and LtrDigest. In contrast to these methods, TE-Learner is the first to incorporate machine learning techniques, outperforming these methods in terms of predictive performance, while able to learn models and make predictions efficiently. Moreover, we show that our method was able to identify TEs that none of the above method could find, and we investigated TE-Learner’s predictions which did not correspond to an official annotation. It turns out that many of these predictions are in fact strongly homologous to a known TE.
Enquiry into the Origin of Our Ideas of the Sublime and Beautiful: Is there a Male Gaze in Empirical Aesthetics?

In his ground-breaking Philosophical Enquiry into the Origin of Our Ideas of the Sublime and Beautiful , Edmund Burke (1757) presented a comprehensive aesthetic theory based on two types of aesthetic appreciation: the beautiful and the sublime. While beauty inspires us with tender feelings of affection, a thrill of delightful horror attracts us to the sublime. According to Burke these ideas originate in a drive for affiliation (beautiful) and a drive for self-preservation (sublime). He also claims that the sublime is generally the more powerful aesthetic experience. A synopsis of literature on gender differences in aesthetic preferences, personality traits, and social motivation suggests, however, that on average women might be less susceptible to the Burkeian sublime than men. We tested this hypothesis empirically using sixty picture details from a triptych by Hieronymus Bosch. One hundred and fifty participants rated these stimuli in terms of threat (respectively safety) and liking. Besides, they completed standardized scales for state and trait anxiety as well as for state and trait depression. We found a strong effect for gender: on average, safety and liking were more closely related for female than for male participants. In the light of these findings we state that Burke’s concepts of the beautiful and the sublime might in fact be confounded with gender-related aesthetic preferences and that his proclivity to the sublime could reflect a male gaze on aesthetics. Finally, we discuss possible indicators for ‘Burke’s fallacy’ in empirical aesthetics today.
Contribution of picoplankton to the total particulate organic carbon concentration in the eastern South Pacific

Abstract. Prochlorococcus, Synechococcus, picophytoeukaryotes and bacterioplankton abundances and contributions to the total particulate organic carbon concentration, derived from the total particle beam attenuation coefficient (cp), were determined across the eastern South Pacific between the Marquesas Islands and the coast of Chile. All flow cytometrically derived abundances decreased towards the hyper-oligotrophic centre of the gyre and were highest at the coast, except for Prochlorococcus, which was not detected under eutrophic conditions. Temperature and nutrient availability appeared important in modulating picophytoplankton abundance, according to the prevailing trophic conditions. Although the non-vegetal particles tended to dominate the cp signal everywhere along the transect (50 to 83%), this dominance seemed to weaken from oligo- to eutrophic conditions, the contributions by vegetal and non-vegetal particles being about equal under mature upwelling conditions. Spatial variability in the vegetal compartment was more important than the non-vegetal one in shaping the water column particle beam attenuation coefficient. Spatial variability in picophytoplankton biomass could be traced by changes in both total chlorophyll a (i.e. mono + divinyl chlorophyll a) concentration and cp. Finally, picophytoeukaryotes contributed ~38% on average to the total integrated phytoplankton carbon biomass or vegetal attenuation signal along the transect, as determined by size measurements (i.e. equivalent spherical diameter) on cells sorted by flow cytometry and optical theory. Although there are some uncertainties associated with these estimates, the new approach used in this work further supports the idea that picophytoeukaryotes play a dominant role in carbon cycling in the upper open ocean, even under hyper-oligotrophic conditions.
The Neuropathology of Head Injury

EDH’s are seen in some 10% of severely head injured patients, 80% being associated with skull fractures and the majority involve the middle meningeal artery with fractures of the squamous temporal bone. SDH’s tend to be more extensive than extradural lesions as blood can spread more freely within the subdural space (Figure 1). The majority are due to disruption of parasagittal bridging veins. ICH’s may be superficial, usually associated with contusions, or they may be more deeply seated, usually within the basal ganglia. When an intracerebral lesion is in continuity with a subdural haematoma the term “burst lobe” is used. Contusions These are seen in approximately 90% of fatal cases of traumatic brain injury, although they may be absent in some 6% of fatal cases. They are more commonly seen at the crests of the frontal and temporal gyri than within sulci and occur principally at sites where the brain comes in contact with the uneven bony surfaces of the base of the skull. Contre-coup lesions on the opposite side of the brain to the site of impact are thought to be due to negative pressures built up as the brain moves in relation to the skull at the moment of impact. Patients with contusions may show sudden clinical deterioration, particularly those with extensive bifrontal lesions.
Differential Contributions of Specimen Types, Culturing, and 16S rRNA Sequencing in Diagnosis of Prosthetic Joint Infections

ABSTRACT Prosthetic joint failure is mainly caused by infection, aseptic failure (AF), and mechanical problems. Infection detection has been improved with modified culture methods and molecular diagnostics. However, comparisons between modified and conventional microbiology methods are difficult due to variations in specimen sampling. In this prospective, multidisciplinary study of hip or knee prosthetic failures, we assessed the contributions of different specimen types, extended culture incubations, and 16S rRNA sequencing for diagnosing prosthetic joint infections (PJI). Project specimens included joint fluid (JF), bone biopsy specimens (BB), soft-tissue biopsy specimens (STB), and swabs (SW) from the prosthesis, collected in situ, and sonication fluid collected from prosthetic components (PC). Specimens were cultured for 6 (conventional) or 14 days, and 16S rRNA sequencing was performed at study completion. Of the 156 patients enrolled, 111 underwent 114 surgical revisions (cases) due to indications of either PJI (n = 43) or AF (n = 71). Conventional tissue biopsy cultures confirmed PJI in 28/43 (65%) cases and refuted AF in 3/71 (4%) cases; one case was not evaluable. Based on these results, minor diagnostic adjustments were made. Fourteen-day cultures of JF, STB, and PC specimens confirmed PJI in 39/42 (93%) cases, and 16S rRNA sequencing confirmed PJI in 33/42 (83%) cases. One PJI case was confirmed with 16S rRNA sequencing alone and five with cultures of project specimens alone. These findings indicated that JF, STB, and PC specimen cultures qualified as an optimal diagnostic set. The contribution of sequencing to diagnosis of PJI may depend on patient selection; this hypothesis requires further investigation.