Miracle-dz/UniFAR-FTUs huggingface dataset:
Abdominal setae and midgut bacteria of the mudshrimp Pestarella tyrrhena

We investigated the diversity of the bacterial 16S rRNA genes occurring on the abdominal setal tufts and in the emptied midgut of the marine mudshrimp Pestarella tyrrhena (Decapoda: Thalassinidea). There were no dominant phylotypes on the setal tufts. The majority of the phylotypes belonged to the phylum Bacteroidetes, frequently occurring in the water column. The rest of the phylotypes were related to anoxygenic photosynthetic α-Proteobacteria and to Actinobacteria. This bacterial profile seems more of a marine assemblage rather than a specific one suggesting that no specific microbial process can be inferred on the setal tufts. In the emptied midgut, 64 clones were attributed to 16 unique phylotypes with the majority (40.6%) belonging to the γ-Proteobacteria, specifically to the genus Vibrio, a marine group with known symbionts of decapods. The next most abundant group was the ɛ-Proteobacteria (28.1%), with members as likely symbionts related to the processes involving redox reactions occurring in the midgut. In addition, phylotypes related to the Spirochaetes (10.9%) were also present, with relatives capable of symbiosis conducting a nitrite associated metabolism. Entomoplasmatales, Bacteroidetes and Actinobacteria related phylotypes were also found. These results indicate a specific bacterial community dominated by putative symbiotic Bacteria within the P. tyrrhena’s midgut.
Customised birthweight standards accurately predict perinatal morbidity

Objective: Fetal growth restriction is associated with adverse perinatal outcome but is often not recognised antenatally, and low birthweight centiles based on population norms are used as a proxy instead. This study compared the association between neonatal morbidity and fetal growth status at birth as determined by customised birthweight centiles and currently used centiles based on population standards. Design: Retrospective cohort study. Setting: Referral hospital, Barcelona, Spain. Patients: A cohort of 13 661 non-malformed singleton deliveries. Interventions: Both population-based and customised standards for birth weight were applied to the study cohort. Customised weight centiles were calculated by adjusting for maternal height, booking weight, parity, ethnic origin, gestational age at delivery and fetal sex. Main outcome measures: Newborn morbidity and perinatal death. Results: The association between smallness for gestational age (SGA) and perinatal morbidity was stronger when birthweight limits were customised, and resulted in an additional 4.1% (n = 565) neonates being classified as SGA. Compared with non-SGA neonates, this newly identified group had an increased risk of perinatal mortality (OR 3.2; 95% CI 1.6 to 6.2), neurological morbidity (OR 3.2; 95% CI 1.7 to 6.1) and non-neurological morbidity (OR 8; 95% CI 4.8 to 13.6). Conclusion: Customised standards improve the prediction of adverse neonatal outcome. The association between SGA and adverse outcome is independent of the gestational age at delivery.
Long-term Outcomes of Anterior Spinal Fusion for Treating Thoracic Adolescent Idiopathic Scoliosis Curves: Average 15-Year Follow-up Analysis

Study Design. Retrospective review. Objective. To assess the long-term outcomes of anterior spinal fusion (ASF) for treating thoracic adolescent idiopathic scoliosis (AIS). Summary of Background Data. Although ASF is reported to provide good coronal and sagittal correction of the main thoracic (MT) AIS curves, the long-term outcomes of ASF is unknown. Methods. A consecutive series of 25 patients with Lenke 1 MT AIS were included. Outcome measures comprised radiographical measurements, pulmonary function, and Scoliosis Research Society outcome instrument (SRS-30) scores (preoperative SRS-30 scores were not documented). Postoperative surgical revisions and complications were recorded. Results. Twenty-five patients were followed-up for 12 to 18 years (average, 15.2 yr). The average MT Cobb angle correction rate and the correction loss at the final follow-up were 56.7% and 9.2°, respectively. The average preoperative instrumented level of kyphosis was 8.3°, which significantly improved to 18.6° (P = 0.0003) at the final follow-up. The average percent-predicted forced vital capacity and forced expiratory volume in 1 second were significantly decreased during long-term follow-up measurements (73% and 69%; P = 0.0004 and 0.0016, respectively). However, no patient had complaints related to pulmonary function. The average total SRS-30 score was 4.0. Implant breakage was not observed. All patients, except 1 who required revision surgery, demonstrated solid fusion. Late instrumentation-related bronchial problems were observed in 1 patient who required implant removal and bronchial tube repair, 13 years after the initial surgery. Conclusion. Overall radiographical findings and patient outcome measures of ASF for Lenke 1 MT AIS were satisfactory at an average follow-up of 15 years. ASF provides significant sagittal correction of the main thoracic curve with long-term maintenance of sagittal profiles. Percent-predicted values of forced vital capacity and forced expiratory volume in 1 second were decreased in this cohort; however, no patient had complaints related to pulmonary function.
Quantitative lineage tracing strategies to resolve multipotency in tissue-specific stem cells

Here, Wuidart et al. present a rigorous new method for assessing the lineage relationship and stem cell fate in different organs and tissues. The authors developed two novel methods for determining lineage relationships: the first one based on statistical analysis of multicolor lineage tracing, and the second one based on lineage tracing at saturation to assess the fate of all stem cells within a given lineage and the “flux” of cells between different lineages.
Rickettsia monteiroi sp. nov., Infecting the Tick Amblyomma incisum in Brazil

ABSTRACT Free-living adult Amblyomma incisum ticks were collected in an Atlantic rainforest area at Intervales State Park, State of São Paulo, Brazil. From an A. incisum specimen, rickettsiae were successfully isolated in Vero cell culture by the shell vial technique. Rickettsial isolation was confirmed by optical microscopy, transmission electron microscopy, and PCRs targeting portions of the rickettsial genes gltA, htrA, rrs, and sca1 on infected cells. Fragments of 1,089, 457, 1,362, and 443 nucleotides of the gltA, htrA, rrs, and sca1 genes, respectively, were sequenced. By BLAST analysis, the partial sequence of rrs of the A. incisum rickettsial isolate was closest to the corresponding sequence of Rickettsia bellii (99.1% similarity). The gltA partial sequence was closest to the corresponding sequences of “Candidatus Rickettsia tarasevichiae” (96.1% similarity) and Rickettsia canadensis (95.8% similarity). The htrA partial sequence was closest to the corresponding sequence of R. canadensis (89.8% similarity). The sca1 partial sequence was closest to the corresponding sequence of R. canadensis (95.2% similarity). Since our rickettsial isolate was genetically distinct from other Rickettsia species, we propose a new species designated Rickettsia monteiroi sp. nov. Phylogenetic analyses indicated that R. monteiroi belongs to the canadensis group within the genus Rickettsia, together with the species R. canadensis and “Candidatus R. tarasevichiae”. Little or no antibody cross-reaction was observed between sera of R. monteiroi-inoculated guinea pigs and R. bellii-, Rickettsia rickettsii-, or R. canadensis-inoculated guinea pigs.
Onset and Progression of Motor Deficits in Motor Neuron Degeneration (mnd) Mice Are Unaltered by the Glycine/NMDA Receptor Antagonist L-701,324 or the MAO-B Inhibitor
 r
 (−)-Deprenyl

NMDA-mediated neurotoxicity and oxidative stress have been implicated in the etiology of a number of degenerative diseases including motor neuron disease. The present study examined the effect of chronic administration of the glycine/NMDA receptor antagonist L-701,324 and the monoamine oxidase B inhibitor (r)-deprenyl on the onset and rate of progression of neurological impairment in the motor neuron degeneration (mnd) mouse, a murine model of neurodegeneration. Neurological assessment of mnd mice revealed an onset of motor deficits at 6 months of age as observed by the loss of hindlimb reflex extension. By 7 months, balance was also markedly impaired as measured by deficits in rotarod performance and ability to remain on balancing beams. At 8 months of age mnd mice exhibited gross abnormalities in walking pattern; animals were unable to flex their hindlimbs and tended to walk in small labored movements. Daily administration of L-701,324 (10 mg/kg p.o.) or r(-)-deprenyl (1 mg/kg p.o.) to mnd mice from 4 to 8 months of age failed to delay the onset of symptoms or slow the rate of deterioration of motor performance. These findings suggest that excessive activation of NMDA receptors may not be involved in the pathological process leading to motor neuron dysfunction in mnd mice and do not suggest a protective effect of deprenyl on motor neurons in these mice.
Estimating Residential and Industrial City Gas Demand Function in the Republic of Korea—A Kalman Filter Application

This paper analyzes the city gas demand function in Korea from 1998 to 2018. The demand function of city gas is derived by a Kalman filter method, and price and income elasticities varying with time are estimated. In the case of residential city gas, the price elasticity gradually decreased to a value of approximately 0.57, while income elasticity increased to approximately 1.48 from 1998 to 2018. Alternatively, industrial city gas demand’s price and income elasticities have been estimated as inelastic, as their absolute values were less than unity over time. The absolute values of price and income elasticities are estimated to be larger for residential than industrial city gas, and thus, city gas consumers are more likely to respond to changes in price and income for residential than industrial city gas. There is a substantial income effect on demand for residential city gas in Korea, whereas industrial city gas is found to have relatively small income and price effects. The results of this study provide policy makers with a Kalman filter method to access more accurate information on the city gas demand function’s elasticities, which change with time.
Single- and alternating-polarization 170-gb/s transmission up to 4000 km using dispersion-managed fiber and all-Raman amplification

We demonstrate transmission of 170-Gb/s single- and alternating-polarization return-to-zero differential phase-shift keying signals in a recirculating loop using dispersion-managed fiber spans and all-Raman amplification. In the single polarization case, bit-error-ratio (BER) values of 5times10-9 and 1.6times10 -4 were obtained after 960 and 2880 km, respectively. In the alternating polarization case, significantly larger transmission distances were achieved, with BER values of 2times10-9 after 1920 km and 5times10-5 after 4320 km, respectively
Dose optimization in CT, in Nuclear Medicine and in PET-CT procedures

The fast development during the last few decades of medical imaging technologies led to the exposure of patients, workers and members of the public to increasingly higher ionizing radiation doses. The assessment of the (radiological) risk versus benefit, arising from the utilization of ionizing radiations for medical imaging purposes, must be performed in light of the three fundamental principles of the international system of Radiation Protection, namely justification, optimization and dose limitation. In this context, the consequences and operational aspects of the implementation of the optimization principle in clinical environments involve complex tasks. For the purposes of the present work, nine Radiology and Nuclear Medicine medical institutions were visited in order to assess the exposure of patients, workers and members of the public to radiation doses in Computed Tomography, conventional Nuclear Medicine and PET/CT examinations.
Uridine 5′-Diphosphate Induces Chemokine Expression in Microglia and Astrocytes through Activation of the P2Y6 Receptor

Chemokines play critical roles in inflammation by recruiting inflammatory cells to injury sites. In this study, we found that UDP induced expression of chemokines CCL2 (MCP-1) and CCL3 (MIP-1α) in microglia, astrocytes, and slice cultures by activation of P2Y6. Interestingly, CCL2 was more highly expressed than CCL3. However, CCL2 synthesis kinetics in response to UDP differed in microglia and astrocytes; microglia rapidly produced small amounts of CCL2, whereas astrocytes continuously synthesized large amounts of CCL2, resulting in a high ultimate level of the chemokine. UDP-induced chemokine expression was reduced in the presence of a specific antagonist of P2Y6 (MRS2578) or small interfering RNA directed against the P2Y6 gene. Inhibition of phospholipase C and calcium increase, downstream signaling pathways of Gq-coupled P2Y6, reduced UDP-induced chemokine expression. UDP activated two calcium-activated transcription factors, NFATc1 and c2. Furthermore, inhibitors of calcineurin (a phosphatase activating NFAT) and NFAT reduced UDP-induced chemokine synthesis. We also found, using a transmigration assay, that UDP-treated astrocytes recruited monocytes. These results suggest that UDP induces chemokine expression in microglia and astrocytes of the injured brain by activation of P2Y6 receptors.
Application of regression and tracing methodology for efficient operation of generators and retailers in a deregulated system

Continuing trend towards deregulation and unbundling of transmission services has resulted in the need to measure the flow of power primarily for pricing and tariff purposes. Tracing methodology hence had been introduced to overcome problems related to the Marginal pricing of transmission costs. This study is twofold: the first revolves around the validation of the method and a 3600 analysis of the proportional method which leads to a redefined power tracing method; the second is to further refine the proposed prediction method by establishing trends of the learning coefficients, using them to examine the relationship between accuracy and number of samples taken. Response of individual generators to change in demand and the corresponding associated losses are also presented. MATLAB with matpower4.0b extension was used to present the study on the IEEE 24bus RTS.
Psychiatric diagnosis in child and adolescent suicide.

BACKGROUND The age, sex, and ethnic distribution of adolescents who commit suicide is significantly different from that of the general population. The present study was designed to examine psychiatric risk factors and the relationship between them and demographic variables. METHODS A case-control, psychologic autopsy study of 120 of 170 consecutive subjects (age, <20 years) who committed suicide and 147 community age-, sex-, and ethnic-matched control subjects who had lived in the Greater New York (NY) area. RESULTS By using parent informants only, 59% of subjects who committed suicide and 23% of control subjects who met DSM-III criteria for a psychiatric diagnosis, 49% and 26%, respectively, had had symptoms for more than 3 years, and 46% and 29%, respectively, had had previous contact with a mental health professional. Best-estimate rates, based on multiple informants for these parameters, for suicides only, were 91%, 52%, and 46%, respectively. Previous attempts and mood disorder were major risks factors for both sexes; substance and/or alcohol abuse was a risk factor for males only. Mood disorder was more common in females, substance and/or alcohol abuse occurred exclusively in males (62% of 18- to 19-year-old suicides). The prevalence of a psychiatric diagnosis and, in particular, substance and/or alcohol abuse increased with age. CONCLUSION A limited range of diagnoses--most commonly a mood disorder alone or in combination with conduct disorder and/or substance abuse--characterizes most suicides among teenagers.
Uses and Abuses of Mathematics in Biology

In the physical sciences, mathematical theory and experimental investigation have always marched together. Mathematics has been less intrusive in the life sciences, possibly because they have until recently been largely descriptive, lacking the invariance principles and fundamental natural constants of physics. Increasingly in recent decades, however, mathematics has become pervasive in biology, taking many different forms: statistics in experimental design; pattern seeking in bioinformatics; models in evolution, ecology, and epidemiology; and much else. I offer an opinionated overview of such uses—and abuses.
Differential Phosphorylation Controls Maskin Association with Eukaryotic Translation Initiation Factor 4E and Localization on the Mitotic Apparatus

ABSTRACT Several cytoplasmic polyadenylation element (CPE)-containing mRNAs that are repressed in Xenopus oocytes become active during meiotic maturation. A group of factors that are anchored to the CPE are responsible for this repression and activation. Two of the most important are CPEB, which binds directly to the CPE, and Maskin, which associates with CPEB. In oocytes, Maskin also binds eukaryotic translation initiation factor 4E (eIF4E), an interaction that excludes eIF4G and prevents formation of the eIF4F initiation complex. When the oocytes are stimulated to reenter the meiotic divisions (maturation), CPEB promotes cytoplasmic polyadenylation. The newly elongated poly(A) tail becomes bound by poly(A) binding protein (PABP), which in turn binds eIF4G and helps it displace Maskin from eIF4E, thereby inducing translation. Here we show that Maskin undergoes several phosphorylation events during oocyte maturation, some of which are important for its dissociation from eIF4E and translational activation of CPE-containing mRNA. These sites are T58, S152, S311, S343, S453, and S638 and are phosphorylated by cdk1. Mutation of these sites to alanine alleviates the cdk1-induced dissociation of Maskin from eIF4E. Prior to maturation, Maskin is phosphorylated on S626 by protein kinase A. While this modification has no detectable effect on translation during oocyte maturation, it is critical for this protein to localize on the mitotic apparatus in somatic cells. These results show that Maskin activity and localization is controlled by differential phosphorylation.
Lycopene content, antioxidant capacity and colour attributes of selected watermelon (Citrullus lanatus (Thunb.) Mansfeld) cultivars grown in India

The present investigation reports variability in lycopene, ascorbic acid, total phenolics, antioxidant capacity and colour attributes of 12 watermelon cultivars grown in India. Antioxidant capacity was evaluated using four in vitro assays, namely ferric reducing antioxidant power, cupric reducing antioxidant capacity, Trolox equivalent antioxidant capacity and 2,2-diphenyl-1-picryl hydrazyl. Among watermelon cultivars, significant differences (p < 0.05) were found with respect to lycopene content and antioxidant capacity. Lycopene content ranged from 03.46 to 8.00 mg/100 g fresh weight. Colour of watermelon flesh was described by an optimized colour index (CI). Cultivars ‘PWM25-4’, ‘Arun’, ‘Kiran’ and ‘Kareena’ were found to be the most promising ones with highest lycopene content, antioxidant capacity and CI. Results indicate that watermelon is a good source of dietary lycopene and there exists significant variation that can be exploited to produce high-quality cultivars.
Evaluation of the mammalian target of rapamycin pathway and the effect of rapamycin on target expression and cellular proliferation in osteosarcoma cells from dogs.

OBJECTIVE To investigate activation of the mammalian target of rapamycin (mTOR) pathway and the antitumor effect of rapamycin in canine osteosarcoma cells. SAMPLE POPULATION 3 established primary canine osteosarcoma cell lines generated from naturally developing tumors. PROCEDURES Expression of total and phosphorylated mTOR and p70S6 kinase was assessed by use of western blot analysis in canine osteosarcoma cells with and without the addition of rapamycin. A clonogenic assay was performed to determine the surviving fraction of osteosarcoma cells at various concentrations of rapamycin. RESULTS Total and phosphorylated mTOR and p70S6 kinase expression was evident in all 3 cell lines evaluated, which was indicative of activation of this pathway. Treatment with rapamycin resulted in a time-dependent decrease in phosphorylated mTOR expression and a lack of detectable phosphorylated p70S6 kinase. No detectable change in expression of total mTOR and total p70S6 kinase was identified after rapamycin treatment. The clonogenic assay revealed a significant dose-dependent decrease in the surviving fraction for all 3 cell lines when treated with rapamycin. CONCLUSIONS AND CLINICAL RELEVANCE These data indicated that mTOR and its downstream product are present and active in canine osteosarcoma cells. The pathway can be inhibited by rapamycin, and treatment of cells with rapamycin decreased the surviving tumor cell fraction. These data support the molecular basis for further investigation into the use of mTOR inhibitors as an antineoplastic approach for dogs with osteosarcoma.
Inter-rater and intra-rater agreement on the Nordic Orofacial Test—Screening examination in children, adolescents and young adults with cerebral palsy

Abstract Objective. To evaluate inter-rater and intra-rater agreement on the Nordic Orofacial Test–Screening (NOT-S) examination applied to children, adolescents and young adults with cerebral palsy (CP). Materials and methods. Using the NOT-S examination, two speech and language pathologists independently assessed video recordings of 48 subjects with CP aged 5–22 years and representing all CP sub-diagnoses and levels of gross motor function and manual ability. Thirty-one subjects were reassessed. Fifteen out of 17 items in the NOT-S examination domains (1) Face at rest, (2) Nose breathing, (3) Facial expression, (4) Masticatory muscle and jaw function, (5) Oral motor function and (6) Speech were rated using a ‘yes’ (dysfunction observed)/‘no’ format, generating an overall score of 0–6. Results. Inter-rater agreement: Twelve out of 15 items and five out of six domains showed acceptable unweighted kappa values (κ = 0.46–1.00). The lowest kappa value was found for domain 4 (κ = −0.04), although it had high inter-rater agreement (92%). The linear weighted kappa value for the overall NOT-S examination score was 0.65 (95% CI = 0.49–0.82). Intra-rater agreement: All items and domains showed acceptable unweighted kappa values (items 0.58–1.00 and 0.59–1.00, domains 0.81–1.00 and 0.62–0.89) for both raters. The linear weighted kappa value for the overall NOT-S examination score was 0.81 (95% CI = 0.63–0.99) for rater A and 0.54 (95% CI = 0.25–0.82) for rater B. Conclusions. The NOT-S examination has acceptable inter-rater and intra-rater agreement when used in young individuals with CP.