Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly Sensitive Molecular Assay for Group A Streptococci Over-Identifies Carriers and May Impact Outpatient Antimicrobial Stewardship.

BACKGROUND Timely, accurate diagnosis of streptococcal (GAS) pharyngitis prevents ARF and limits antibiotic overuse. The Illumigene® Group A Streptococcus assay (Meridian Bioscience) is a molecular test for GAS pharyngitis with high sensitivity and specificity. We sought to determine whether the Illumigene test is more likely than throat culture to be positive in patients without pharyngeal symptoms and explore the limits of detection of the test. METHODS Patients aged 3-17 years were eligible if they had no history of pharyngitis or use of antibiotics within the previous 2 weeks; there were no URI symptoms, sore throat, or fever; and no signs of infection. Culture and Illumigene were performed on duplicate throat swabs. Excess lysate from a subset of Illumigene tests was evaluated by RT-PCR. IRB-approval was obtained. RESULTS We enrolled 385 patients from 2/2016 through 10/2017; mean age was 10yrs; 51% were male. Most visits were for health supervision (69%). Significantly more Illumigene tests (78/385, 20.3%) than throat cultures (48/385, 12.5%) were positive (χ, p=.0035). Illumigene was "indeterminate" for 3 patients, leaving 382 pairs of swabs for analysis. Results were discordant for 32/382 pairs (8.4%); 31/32 (97%) were Illumigene-positive/culture-negative (McNemar's test, p<.000001). RT-PCR was negative in 4/13 (31%) tested Illumigene-positive lysates; the paired culture had been negative in all four. The limit of detection for the Illumigene test was 55 CFU/ml. CONCLUSIONS The Illumigene test is significantly more likely than throat culture to yield positive results in patients without GAS pharyngitis. Failure to appropriately select patients for testing may negatively impact antimicrobial stewardship efforts without benefit to patients.
Cytogenetics of wild and captive bred non-domestic animals

Cytogenetics of wild and captive bred non-domestic animals provides us with valuable information that can be implemented in wildlife management and species conservation strategies. In this review, we summarized the data published to date describing a range of chromosome abnormalities observed in non-domestic animals and their effect on phenotype. Two important factors that can potentially have drastic effects on captive breeding programs are discussed: presence of classic chromosome abnormalities, spontaneously-occurring and inherited, and intraspecific variations in chromosome number. Short-term consequences, primarily reduced reproductive efficiency, and long-term consequences, such as changes in population dynamics, are examined.
Risk and Protective Environmental Factors Associated with Autism Spectrum Disorder: Evidence-Based Principles and Recommendations

Autism Spectrum Disorder (ASD) is a complex condition with early childhood onset, characterized by a set of common behavioral features. The etiology of ASD is not yet fully understood; however, it reflects the interaction between genetics and environment. While genetics is now a well-established risk factor, several data support a contribution of the environment as well. This paper summarizes the conclusions of a consensus conference focused on the potential pathogenetic role of environmental factors and on their interactions with genetics. Several environmental factors have been discussed in terms of ASD risk, namely advanced parental age, assisted reproductive technologies, nutritional factors, maternal infections and diseases, environmental chemicals and toxicants, and medications, as well as some other conditions. The analysis focused on their specific impact on three biologically relevant time windows for brain development: the periconception, prenatal, and early postnatal periods. Possible protective factors that might prevent or modify an ASD trajectory have been explored as well. Recommendations for clinicians to reduce ASD risk or its severity have been proposed. Developments in molecular biology and big data approaches, which are able to assess a large number of coexisting factors, are offering new opportunities to disentangle the gene–environment interplay that can lead to the development of ASD.
Functional definition of NrtR, a remnant regulator of NAD+ homeostasis in the zoonotic pathogen Streptococcus suis

NAD+ is an enzyme cofactor required for the 3 domains of life. However, little is known about the NAD+ biosynthesis and salvage pathways in the opportunistic pathogen Streptococcus suis. A genome‐wide search allows us to identify the NAD+ salvage pathway encoded by an operon of nadR‐pnuC‐nrtR (from SSU05_1973 to SSU05_1971 on the reverse strand) in the S. suis 05ZYH33 that causes streptococcal toxin shock–like syndrome. The regulator of this pathway is Nudix–related transcriptional regulator (NrtR), a transcription regulator of the Nudix family comprising an N‐terminal Nudix‐like effector domain, and a C‐terminal DNA‐binding winged helix‐turn‐helix–like domain. Intriguingly, the S. suis NrtR naturally contains a single amino acid substitution (K92E) in the catalytic site of its Nudix domain that renders it catalytically inactive but does not influence its ability to bind DNA. Despite its lack of enzymatic activity, DNA‐binding activity of NrtR is antagonized by the effector ADP‐ribose. Furthermore, nrtR knockout in S. suis serotype 2 reduces its capacity to form biofilms and attenuates its virulence in a mouse infection model. Genome mining indicates that nrtR appears in a strain‐specific manner whose occupancy is correlated to bacterial infectivity. Unlike the paradigmatic member of NrtR family having 2 unrelated functions (Nudix hydrolase and DNA binding), S. suis 2 retains a single regulatory role in the modulation of NAD+ salvage. This control of NAD+ homeostasis contributes to S. suis virulence. —Wang, Q. , Hassan, B. H. , Lou, N. , Merritt, J., Feng, Y. Functional definition of NrtR, a remnant regulator of NAD+ homeostasis in the zoonotic pathogen Streptococcus suis. FASEB J. 33, 6055–6068 (2019). www.fasebj. org
Division- and Addition-Based Models of Rhythm in a Computer-Assisted Composition System

Reading descriptions of different musical traditions or of the practice of different individual composers, it is not uncommon to see a rhythmic idiom described as "additive/7 meaning in simple terms that it consists of durations formed by combining, or adding together, the units provided by a rapid underlying pulse (Koetting 1970; Pratt 1987; Clayton 2000). Such a characterization distinguishes the rhythmic idiom from others involving the division of the units of some referential pulse into variable numbers of smaller parts, an important feature of tonal Western classical music (Lerdahl and Jackendoff 1983). My present concern is not the ability of additionor division-based models of rhythm to accurately describe existing musical traditions, but the value of these models as a basis for generating rhythms in an algorithmic-composition system, in which potentially novel rhythmic idioms may be sought. In particular, I will describe a series of algorithms I have used in my own work as a composer, and I will investigate some of the advantages and disadvantages each of these algorithms inherits from the particular model of rhythm on which it is based. The development of these algorithms was shaped by at least two compositional goals to create music for human performance, and to express it using common-practice Western music notation (Byrd 1994). My investigations will be made in the context of the same goals. For the sake of making the distinction between the two types of models clearer, Figure 1 presents simple illustrations of rhythms generated by purely addition-based and purely division-based means. In Figure la, the upper row of the diagram represents a stream of timespans constituting the units of some isochronous pulse. The lower row of this diagram shows these timespans grouped into durations of 3, 5, 3, 2, 5, and 2 units to constitute the resulting rhythm. (These values are labeled in the diagram, but of course we could also count unit pulses to determine them.) Although the resulting rhythm lacks the isochrony of the original unit pulse, we can treat it like another pulse and combine adjacent timespans to form larger durations. In this way, the additive process is capable of forming hierarchies of timespans deeper than the two levels illustrated here.
Red and near‐infrared light induces intracellular Ca2+ flux via the activation of glutamate N‐methyl‐D‐aspartate receptors

Red and near‐infrared (NIR) light effect on Ca2+ ions flux through the influence on N‐methyl‐D‐aspartate receptors (NMDARs) and their functioning in HeLa cells was studied in vitro. Cells were irradiated by 650 and 808 nm laser light at different power densities and doses and the obtained effect was compared with that caused by the pharmacological agents. The laser light was found to elevate Ca2+ influx into cell cytoplasm in a dose‐dependent manner without changes of the NMDAR functioning. Furthermore, the light of both wavelengths demonstrated the ability to elevate Ca2+ influx under the pharmacological blockade of NMDARs and also might partially abolish the blockade enhancing Ca2+ influx after selective stimulation of the receptors with NMDA. Simultaneously, the light at moderate doses demonstrated a photobiostimulating effect on cells. Based on our experiments and data reported in the literature, we suggest that the low‐power visible and NIR light can instigate a cell membrane depolarization via nonthermal activation, resulting in the fast induction of Ca2+ influx into cells. The obtained results also demonstrate that NIR light can be used for nonthermal and nonpharmacological stimulation of NMDARs in cancer cells.
Detection of free intraperitoneal tumour cells in peritoneal lavage fluid from patients with peritoneal metastasis before and after treatment with pressurised intraperitoneal aerosol chemotherapy (PIPAC)

Aims In this study, we investigated whether free intraperitoneal tumour cells (FITC) were detectable in ascites or peritoneal lavage fluid (PLF) from patients with peritoneal metastasis (PM) before and after treatment with pressurised intraperitoneal aerosol chemotherapy (PIPAC). Methods Ascites or PLF retrieved at the first and third PIPAC procedures was analysed by conventional cytology, carcinoembryonic antigen (CEA) and total protein concentration, and quantitative reverse transcriptase PCR (qRT-PCR) for mRNA expression of CEA, epithelial cell adhesion molecule (EpCAM) and cancer antigen 125 (CA-125). Conventional cytology and qRT-PCR were also performed in a negative control group (benign PLF specimens and inflammatory ascites). The treatment response was compared with the histological response based on repeated peritoneal biopsies evaluated by the Peritoneal Regression Grading Score (PRGS). Results Thirty-five patients with PM of various origins were included from 2015 to 2016. At the first PIPAC procedure, FITC were detected by conventional cytology (sensitivity 0.58, specificity 1.00), CEA protein (cut-off 0.4 µg/L, sensitivity 0.71), CEA mRNA (sensitivity 0.75, specificity 1.00), EpCAM mRNA (sensitivity 0.71, specificity 1.00) and CA-125 mRNA (sensitivity 0.43, specificity 1.00). The combination of CEA/EpCAM mRNA had a sensitivity of 0.88 and a specificity of 1.00. The evaluation of ascites or PLF retrieved at the third PIPAC procedure failed to detect treatment response, when compared with the histological PRGS. Conclusions The evaluation of CEA and EpCAM mRNA detects FITC with a high sensitivity and an excellent specificity, but is not useful for response evaluation in patients treated with PIPAC. Trial registration number NCT02320448.
Muscle-specific color stability in fresh beef from grain-finished Bos indicus cattle

Objective To investigate the color and oxidative stabilities of longissimus lumborum (LL) and psoas major (PM) muscles from grain-finished Bos indicus cattle in Brazil. Methods The LL and PM muscles were obtained 24 h post-mortem from eight (n = 8) Nellore bull carcasses, fabricated into 1.5-cm steaks, aerobically packaged, and stored at 4°C for nine days. Steaks were analyzed for myoglobin concentration, pH, instrumental color, metmyoglobin reducing activity (MRA) and lipid oxidation. Results The LL steaks exhibited greater (p<0.05) redness, color stability, and MRA than their PM counterparts on days 5 and 9. The LL and PM steaks demonstrated similar (p>0.05) lightness and yellowness on days 0, 5, and 9. On the other hand, PM steaks exhibited greater (p<0.05) myoglobin concentration, pH, and lipid oxidation than their LL counterparts. Conclusion These results indicated that muscle source influenced the color and oxidative stabilities of beef from grain-finished Bos indicus animals. These results highlighted the necessity of muscle-specific strategies to improve the color stability of beef from grain-fed Bos indicus cattle.
AmpI Functions as an Iron Exporter To Alleviate β-Lactam-Mediated Reactive Oxygen Species Stress in Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is an organism with a remarkable capacity for drug resistance with several antibiotic resistance determinants in its genome. S. maltophilia genome codes for L1 and L2, responsible for intrinsic β-lactam resistance. ABSTRACT Stenotrophomonas maltophilia is an organism with a remarkable capacity for drug resistance with several antibiotic resistance determinants in its genome. S. maltophilia genome codes for L1 and L2, responsible for intrinsic β-lactam resistance. The Smlt3721 gene (denoted ampI), located downstream of the L2 gene, encodes an inner membrane protein. The existence of an L2 gene-ampI operon was verified by reverse transcription-PCR (RT-PCR). For aerobically grown S. maltophilia KJ, inactivation of ampI downregulated siderophore synthesis and iron acquisition systems and upregulated the iron storage system, as demonstrated by a transcriptome assay, suggesting that AmpI is involved in iron homeostasis. Compared with the wild-type KJ, an ampI mutant had an elevated intracellular iron level, as revealed by inductively coupled plasma mass spectrometry (ICP-MS) analysis, and increased sensitivity to H2O2, verifying the role of AmpI as an iron exporter. The β-lactam stress increased the intracellular reactive oxygen species (ROS) level and induced the expression of the L1 gene and L2 gene-ampI operon. Compared to its own parental strain, the ampI mutant had reduced growth in β-lactam-containing medium, and the ampI mutant viability was improved after complementation with plasmid pAmpI in either a β-lactamase-positive or β-lactamase-negative genetic background. Collectively, upon challenge with β-lactam, the inducibly expressed L1 and L2 β-lactamases contribute to β-lactam resistance by hydrolyzing β-lactam. AmpI functions as an iron exporter participating in rapidly weakening β-lactam-mediated ROS toxicity. The L1 gene and L2 gene-ampI operon enable S. maltophilia to effectively cope with β-lactam-induced stress.
The contribution of semantic memory to the recognition of basic emotions and emotional valence: Evidence from the semantic variant of primary progressive aphasia

ABSTRACT There is compelling evidence that semantic memory is involved in emotion recognition. However, its contribution to the recognition of emotional valence and basic emotions remains unclear. We compared the performance of 10 participants with the semantic variant of primary progressive aphasia (svPPA), a clinical model of semantic memory impairment, to that of 33 healthy participants using three experimental tasks assessing the recognition of: 1) emotional valence conveyed by photographic scenes, 2) basic emotions conveyed by facial expressions, and 3) basic emotions conveyed by prosody sounds. Individuals with svPPA showed significant deficits in the recognition of emotional valence and basic emotions (except happiness and surprise conveyed by facial expressions). However, the performance of the two groups was comparable when the performance on tests assessing semantic memory was added as a covariate in the analyses. Altogether, these results suggest that semantic memory contributes to the recognition of emotional valence and basic emotions. By examining the recognition of emotional valence and basic emotions in individuals with selective semantic memory loss, our results contribute to the refinement of current theories on the role of semantic memory in emotion recognition.
Consultant Pharmacist–Provider Collaboration in U.S. Assisted Living Facilities: A Pilot Study

The purpose of this pilot study was to explore the impact of pharmacist-provided recommendations to general practitioners (GPs) of patients living in assisted living facilities (ALFs). A secondary objective of this study was to explore prescriber and ALF staff perceptions. This was a mixed-method, quasi experimental 1-group pre/post-test study with an explanatory qualitative arm using in-depth semi-structured interviews at five regional ALFs and one independent community pharmacy in East Tennessee. Residents older than 65 years of age, with confirmed diagnosis of Type II diabetes in the pharmacy’s medical record, taking anti-diabetic medication for at least 14 days and resident of affiliated ALF for at least past 30 days were enrolled. Phase 1 demonstrated a 35.1% (13/37 recommendations) acceptance rate of pharmacist recommendations. Phase 2 demonstrated a similar 31.3% acceptance rate of pharmacist recommendations (5/16 recommendations). The mean pre–post difference in average 30-day FBG was greater in the accepted group than the rejected recommendation group (−9.1 vs. −2.3 mg/dL). Pharmacist–GP collaboration in the ALF population was feasible and may improve the quality of patient care of these residents.
Anophthalmos, microphthalmos, and typical coloboma in the United Kingdom: a prospective study of incidence and risk.

PURPOSE Anophthalmos, microphthalmos, and typical coloboma (AMC) form an interrelated spectrum of congenital eye anomalies that can cause significant visual loss and cosmetic disfigurement in children. This prospective study of children born in the United Kingdom was undertaken to determine the incidence of AMC diagnosed by ophthalmologists and to explore sociodemographic risks. METHODS Recruitment was achieved though an established active surveillance system of U.K. ophthalmologists supported by a new research network of interested specialists, the Surveillance of Eye Anomalies (SEA-UK) Special Interest Group. It started October 1, 2006, and continued over 18 months. RESULTS One hundred thirty-five children were newly diagnosed with AMC. Typical colobomatous defects were the commonest phenotype, and anophthalmos was rare (n = 7). Both eyes were affected in 55.5% of the children. The cumulative incidence of AMC by age 16 years was 11.9 per 100,000 (95% CI, 10.9-15.4). Of the children examined, 41.5% had not seen an ophthalmologist by 3 months of age. The incidence in Scotland was nearly double that in England and Wales. The children of Pakistani ethnicity had a 3.7 (95% CI, 1.9-7.5) times higher risk of AMC than did white children. There was some evidence to suggest a higher incidence in the more socioeconomically deprived. The sibling risk ratio was 210 (95% CI, 25-722). CONCLUSIONS This is the first prospective study of AMC, and it establishes the frequency across the United Kingdom. Comparisons with data quoted in the literature are difficult because study methodologies differ, but the frequency appears to be lower than that quoted for other developed countries. There are geographic and ethnic variations in incidence that warrant further investigation.
Small animal disease surveillance: gastrointestinal disease, antibacterial prescription and Tritrichomonas foetus

#### Gastrointestinal disease, antibacterial prescription and Tritrichomonas foetus : Report summary This report represents the third time the Small Animal Veterinary Surveillance Network (SAVSNET) has summarised gastrointestinal (GI) disease in companion animals.1,2 The present report considers electronic health records (EHRs) captured by the SAVSNET project from 236 voluntary veterinary practices (526 sites) over a 19-month period from 1 April 2017 to 31 October 2018. A detailed description of the methodology used by SAVSNET to capture EHRs has been provided previously.2,3 A total of 2,231,928 consultations were analysed, of which 69.8 per cent were from dogs, 26.8 per cent were from cats, 1.7 per cent were from rabbits, and the remaining 1.6 per cent were from other species, or where species was not recorded. Animals mainly presenting for investigation and/or treatment of GI disease according to the attending veterinary surgeon or …
Immediately Loaded Fixed Full-Arch Implant-Retained Prosthesis: Clinical Analysis When Using a Moderate Insertion Torque.

PURPOSE This study uses intentionally tilted implants with a moderate insertion torque to retain an immediately loaded fixed full-arch implant-retained prosthesis using four implants. The aims of this study were to determine the likelihood that this type of implant-retained prosthesis can be predictably provided on the day of implant placement, the survival rate when providing immediate load, and the importance of insertion torque on the survival of the implants. MATERIALS AND METHODS All implants that were placed after August 1, 2015 and before December 31, 2016 at the ClearChoice Dental Implant Center of Minneapolis were recorded. The performance of these implants was followed to determine the success rate in the category of "intention to treat" where the treatment is provided on the same day as implant placement. Insertion torque was recorded for all implants. Implants were followed to determine survival of the implants and complications observed. RESULTS Between August 1, 2015 and December 31, 2016, a total of 1,903 implants were placed. These implants were utilized to support 441 prostheses, with 440 actually being restored with a provisional prosthesis on the day of implant placement. Mean follow-up time was 484 days with a maximum of 972 days and a median of 474 days. A total of 36 implants failed to achieve osseointegration, resulting in an overall survival rate of 98.1% with a confidence interval (CI) of 98.7% to 97.5%. Survival was 97.6% in the maxilla and 98.9% in the mandible. Insertion torque of less than 15 Ncm (n = 80, 77 survival), between 15 and 34 Ncm (n = 122, 120 survival), and greater than 35 Ncm (n = 1,701, 1,670 survival) demonstrated no difference in implant survival. CONCLUSION Based on this study of 1,903 implants placed between August 1, 2015 and December 31, 2016, the following observations were made: (1) this surgical/prosthetic treatment approach succeeded in the "intention to treat" category with 440/441 (99.8%) prostheses inserted on the day of implant surgery; (2) overall implant survival was 98.1%; (3) insertion torque appeared to have no effect on implant survival.