Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Clostridioides difficile-inhibiting gut commensals using culturomics, phenotyping, and combinatorial community assembly

A major function of the gut microbiota is to provide colonization resistance, wherein pathogens are inhibited or suppressed below infectious level. However, the fraction of gut microbiota required for colonization resistance remains unclear. We used culturomics to isolate a gut microbiota culture collection comprising 1590 isolates belonging to 102 species. Estimated by metagenomic sequencing of fecal samples used for culture, this culture collection represents 50.73% of taxonomic diversity and 70% functional capacity. Using whole genome sequencing we characterized species representatives from this collection, and predicted their phenotypic traits, further characterizing isolates by defining nutrient utilization profile and short chain fatty acid (SCFA) production. When screened using a co-culture assay, 66 species in our culture collection inhibited C. difficile. Several phenotypes, particularly, growth rate, production of SCFAs, and the utilization of mannitol, sorbitol or succinate correlated with C. difficile inhibition. We used a combinatorial community assembly approach to formulate defined bacterial mixes inhibitory to C. difficile. When 256 combinations were tested, we found both species composition and blend size to be important in inhibition. Our results show that the interaction of bacteria with each other in a mix and with other members of gut commensals must be investigated for designing defined bacterial mixes for inhibiting C. difficile in vivo. IMPORTANCE Antibiotic treatment causes instability of gut microbiota and the loss of colonization resistance, allowing pathogens such as C. difficile to colonize, causing recurrent infection and mortality. Although fecal microbiome transplantation has shown to be an effective treatment for C. difficile infection (CDI), a more desirable approach would be the use of a defined mix of inhibitory gut bacteria. C. difficile-inhibiting species and bacterial combinations we identify herein improve our understanding of the ecological interactions controlling colonization resistance against C. difficile, and could aid the design of defined bacteriotherapy as a non-antibiotic alternative against CDI.
PAEDIATRIC UTI: POINTS OF CONCERN: A CLINICOBACTERIOLOGICAL ANALYSIS IN A TERTIARY CARE HOSPITAL

Paediatric UTI is a matter of grave concern particularly at less than two years of age due to predisposition to serious future complications and limited treatment options resulting from ever-increasing antibiotic resistance. This study included 392 established cases of paediatric UTI. Gram negative bacteria were isolated in 68.9% cases, predominated by Escherichia coli (34.7%). It was followed by Klebsiella species (27.3%), Enterococcus faecalis (12.2%), Acinetobacter species (7.4%), Pseudomonas aeruginosa (4.3%), and other GNB. Staphylococcus saprophyticus (4.1%) and Staphylococcus aureus (3.1%) were less common. Antibiograms of the isolates showed very low sensitivity to all commonly prescribed antibiotics, namely, ampicillin, amoxyclav, ceftriaxone, cefotaxime, gentamicin, cotrimoxazole, nitrofurantoin, ciprofloxacin and levofloxacinmaking them practically irrational to choose. Most of the GNB were susceptible to imipenem, whereas, gram positive cocci were uniformly susceptible to vancomycin and linezolid.
Spatial control of nucleoporin assembly by Fragile X-related proteins

Nucleoporins (Nups) build highly organized Nuclear Pore Complexes (NPCs) at the nuclear envelope (NE). Several Nups assemble into a sieve-like hydrogel within the central channel of the NPCs to regulate nucleocytoplasmic exchange. In the cytoplasm, a large excess of soluble Nups has been reported, but how their assembly is restricted to the NE is currently unknown. Here we show that Fragile X-related protein 1 (FXR1) can interact with several Nups and facilitate their localization to the NE during interphase through a microtubule and dynein-dependent mechanism. Downregulation of FXR1 or closely related orthologs FXR2 and Fragile X mental retardation protein (FMRP) leads to the accumulation of cytoplasmic Nup protein condensates. Likewise, several models of Fragile X syndrome (FXS), characterized by a loss of FMRP, also accumulate cytoplasmic Nup aggregates. These aggregate-containing cells display aberrant nuclear morphology and a delay in G1 cell cycle progression. Our results reveal an unexpected role for the FXR protein family and dynein in the spatial regulation of nucleoporin assembly. Highlights Cytoplasmic nucleoporins are assembled by Fragile X-related (FXR) proteins and dynein FXR-Dynein pathway downregulation induces aberrant cytoplasmic aggregation of nucleoporins Cellular models of Fragile X syndrome accumulate aberrant cytoplasmic nucleoporin aggregates. FXR-Dynein pathway regulates nuclear morphology and G1 cell cycle progression eTOC Blurb Nucleoporins (Nups) form Nuclear Pore Complexes (NPCs) at the nuclear envelope. Agote-Arán at al. show how cells inhibit aberrant assembly of Nups in the cytoplasm and identify Fragile X-related (FXR) proteins and dynein that facilitate localization of Nups to the nuclear envelope and control G1 cell cycle progression. Graphical abstract
Phytochemical and Ecological Analysis of Two Varieties of Hemp (Cannabis sativa L.) Grown in a Mountain Environment of Italian Alps

Hemp (Cannabis sativa L.) is a multifunctional crop that is capable of prompt environmental adaptation. In this study, a monoecious cultivar (Futura 75) and a dioecious one (Finola) were tested in a mountain area in Valsaviore (Rhaetian Alps, Italy; elevation: 1,100 m a.s.l.) during the growing season 2018. Phytochemical behavior was evaluated by different analytical approaches: HPLC-high-resolution mass spectrometry, SDS-PAGE LC-MS/MS, HS-SPME GC-MS, and GC-FID in order to obtain complete profile of two varieties cultivated in altitude. CSR functional strategy used for ecological evaluation revealed that both genotypes are mainly competitors, although Finola is more stress tolerator (C:S:R = 57:26:17%) than Futura (C:S:R = 69:15:16%). The Finola inflorescences were characterized by higher quantities of β-ocimene and α-terpinolene, while α- and ß-pinene accompanied by extremely high ß-myrcene were found as predominant in Futura. Both varieties were rich in sesquiterpenes (45 recognized) among which trans-caryophyllene and α-humulene were the most abundant. Total tetrahydrocannabinol level was lower than 0.1%, while the most abundant cannabinoid was cannabidiolic acid (CBDA): 2.3% found in Finola vs. 2.7% revealed for Futura. The level of corresponding neutral form, cannabidiol, varied drastically: 0.27% (Finola) vs. 0.056% (Futura). Finola showed the unique cannabinoid profile with unexpectedly high cannabidivarin, 2-fold higher that corresponding acidic analogue, whereas the particularity of Futura 75 was the occurrence of cannabigerolic acid (CBGA) in the quantities that was double than those exposed for Finola. The seeds from both chemovars proved to be rich in polyunsaturated fatty acids, and Finola showed a higher ratio ω6/ω3. No difference was found in the protein content, and the SDS-PAGE profile was similar. The most abundant protein was edestin, followed by heat shock protein 70, ß-conglycinin, and vicilin. In conclusion, comprehensive phytochemical and ecological study of two fiber-type varieties cultivated in Italian Alps displayed specific, legal, and safe cannabinoids profile, followed by particular terpene composition, polyunsaturated fatty acids content, and favorable protein profile. This postulates that geographical provenience of hemp should be considered in selecting a variety that would be suitable for a specific end-use nutraceutical application.
Diabetics with Obstructive Sleep Apnea need Higher Positive Airway Pressures

Introduction: Continuous positive airway pressure (CPAP) is the only proven therapy for moderate to severe obstructive sleep apnea syndrome (OSAS). The CPAP requirements can widely vary among individuals. We studied the demographic, clinical, and polysomnographic (PSG) predictors of high CPAP requirement (pressures >10 cm H 2 O) in a cohort of patients with OSAS. Materials and methods: Consecutive patients with PSG-proven moderate to severe OSAS attending the Sleep Clinic, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India, were prospectively recruited for the study from November 2014 till October 2015. After informed consent, demographic data, risk factor profile, and PSG data were extracted using a structured pro forma. All the patients underwent overnight CPAP titration in the sleep laboratory as per guidelines. The patients were grouped into two, those requiring CPAP ≤ 10 and >10 cm H 2 O. Pearson correlation and chi square tests were used to study the association between variables. Results: A total of 64 patients (55 male, 9 female) with OSAS underwent CPAP titration during the study period. Mean age of the study group was 53.81 ± 12.01 (26–85 years) and majority were overweight by Asian standards [mean body mass index (BMI) 29.31 ± 5.01]. Mean apnea-hypopnea index (AHI) of the cohort was 62.28. Average CPAP requirement was 11.82 cm H 2 O. We found that neck circumference, presence of diabetes mellitus (DM), and AHI severity were independent predictors for higher PAP requirements, while gender, BMI, and other vascular risk factors were not predictive of high PAP requirements. Conclusion: Diabetes mellitus and neck circumference are better predictors of higher CPAP requirements in Indian population than BMI. Those with higher AHI required more pressures while apnea duration failed to show an association with higher PAP. Radhakrishnan Diabetics with Obstructive Sleep Apnea need Higher Positive Airway Pressures.
Genomic interrogation of the burden and transmission of multidrug-resistant pathogens within and across hospital networks

Background Multidrug-resistant organisms (MDROs) disproportionately affect hospitalized patients due to the combination of comorbidities, frequent antimicrobial use, and in-hospital MDRO transmission. Identification of MDRO transmission by hospital microbiology laboratories is difficult due to limitations of existing typing methods. Methods We conducted a prospective multicenter genomics implementation study (8 hospitals, 2800 beds) from 24th April to 18th June 2017 in Melbourne, Australia. Clinical and screening isolates from hospital inpatients were collected for six MDROs (vanA VRE, MRSA, ESBL E. coli [ESBL-Ec] and Klebsiella pneumoniae [ESBL-Kp], and carbapenem-resistant Pseudomonas aeruginosa [CRPa] and Acinetobacter baumannii [CRAb]), sequenced (Illumina NextSeq) and analyzed using open-source tools. MDRO transmission was assessed by genomics (core SNP phylogeny, grouped by species and ST) and compared to epidemiologic data. Results 408 isolates were collected from 358 patients; 47.5% were screening isolates. ESBL-Ec was most common (52.5%), then MRSA (21.6%), vanA VRE (15.7%) and ESBL-Kp (7.6%). We define the transmission rate for each MDRO by genomics and epidemiology; 31.6% of all study patients had potential genomic links to other study isolates; 86% of these were confirmed by epidemiologic links (probable or possible transmission). The highest transmission rates occurred with vanA VRE (88.4% of patients). Conclusions Combining genomics with high-quality epidemiologic data gives substantial insights into the burden and distribution of critical MDROs in hospitals, including in-hospital transmission. By defining transmission rates by genomics, we hope to enable comparisons over time and between sites, and introduce this as a new outcome measure to assess the efficacy of infection control interventions.
Platelet Inhibition to Target Reperfusion Injury (The PITRI trial): Rationale and Study Design.

Heerajnarain Bulluck PhD, Mervyn Chan BSc, Jennifer Bryant PhD, Ping Chai MBBS, Ashish Chawla MBBS, Terrance Chua MBBS, Yiu-Cho Chung PhD, Gao Fei PhD, Hee Hwa Ho MBBS, Andrew Fu Wah Ho MBBS, Andrew John Hoe MBBS, Syed Saqib Imran MBBS, Ronald Lee MBBS, Swee Han Lim MBBS, Boon Wah Liew MBBS, Patrick Lim Zhan Yun MBBS, Marcus Ong Eng Hock MBBS, Valeria Paradies MD, Matthew T Roe MD, Lynette Teo MBBS, Aaron Wong MBBS, Evelyn Wong MBBS, Philip Wong MBBS, Timothy Watson MBBS, Mark Y Chan PhD, Jack W Tan MBBS, Derek J Hausenloy PhD
Efficacy and suitability of whole wheat flour on the growth and survival of Rohu (Labeo rohita)

The efficacy and suitability of dietary whole wheat flour supplementation was evaluated on the growth performance and survival of rohu (Labeo rohita). The study was conducted in 12 experimental aquaria at the Wet Laboratory, Department of Aquaculture, Bangladesh Agricultural University, Mymensingh. A total of 180 fingerlings of mean initial weight of 1.744±00 g were stocked at the same stocking density (268 fingerlings/m3). Four different treatments (T1, T2, T3 and T4) each with three replications were performed having different level of whole wheat flour such as 0% whole wheat flour (T1), 5% whole wheat flour (T2), 10% whole wheat flour (T3) and 15% whole wheat flour (T4). Feeds were supplied at 5% body weight twice daily in the morning at 9.00 am and in the afternoon at 5.00 pm throughout the study period. The rations were adjusted every week when new weights of the fish for various experimental aquariums were determined. At the end of the 63 days study period, the growth performance parameters such as mean final weight (g), weight gain (g), percent weight gain (%), specific growth rate (%/day) and the best feed utilization in terms of food conversion ratio were found highest at treatment 4 where fishes were fed with inclusion of 15% whole wheat flour and lowest was found at treatment 1 (fed with inclusion of 0% whole wheat flour). Water quality parameters were within the acceptable range and survival rate was found 100% in all treatment. Therefore, it can be concluded that treatment 4 (highest growth performance and survival rate of L. rohita with supplementation of 15% whole wheat flour containing diet) can be chosen by fish farmers for commercial culture of this species. Res. Agric. , Livest. Fish.6(2): 345-352, August 2019
Primary adrenal insufficiency secondary to bilateral adrenal lymphoma

Involvement of adrenal glands in lymphoma is rare; the patient may have variable presentations. We report a case of a 62-year-old Saudi female who presented to our center with a few-week history of fatigue, weight loss, subjective fever, and a recent change in skin color. On examination, she looked dehydrated and had a drop in blood pressure with postural change and hyperpigmentation of the skin of the face and hands. Morning cortisol levels were low, and adrenocorticotropic hormone levels were high, which indicated primary adrenal insufficiency (PAI). An adrenal computed tomography (CT) scan revealed bilateral adrenal enlargement. After excluding pheochromocytoma, a CT scan-guided trucut biopsy of the adrenals confirmed non-Hodgkin lymphoma. The patient was started on steroid replacement therapy, and after stabilization, a plan was made to initiate chemotherapy for the treatment of lymphoma; unfortunately, the patient died shortly after diagnosis because of rapid progression of the disease. Adrenal lymphoma can present with PAI and should be considered in the presence of bilateral adrenal enlargement; it is an aggressive tumor and carries poor prognosis if the treatment is delayed.
In-water methods reveal population dynamics of a green turtle Chelonia mydas foraging aggregation in the Philippines

The green turtle Chelonia mydas is an Endangered species that forms aggregations at neritic foraging sites where juveniles spend, in some cases, over a decade before moving to adultor subadult-dominated foraging sites. Here, we used photographic identification, behavioural observations, paired-laser and stereo-photogrammetry to determine the population dynamics of a coastal aggregation of green turtles in Oslob, Philippines. We identified a total of 82 individual turtles between May 2012 and October 2018. We recorded behavioural observations during individual identification and found that turtles changed behaviour in 25% of instances. Some turtles were identified consistently throughout the study period, indicating strong site fidelity and residency. Modified maximum likelihood models suggest turtles spend the majority of their time within the study area (>92%), although some (8%) excursions outside the area do occur. Markrecapture models suggest this foraging aggregation exhibits a pattern similar to that of a closed population. This is likely due to the extended residency periods of some individuals at the site, and the relatively low recruitment rate over time. We measured 18 turtles using paired-laser photo grammetry, with estimated straight carapace length of 55.3 cm, and mean growth rates of 3.4 cm yr−1. Stereo-photogrammetry measurements were consistent and more accurate than visual or paired-laser photogrammetry estimates. Our results highlight the use of in-water methods to understand population dynamics of green turtles, and the importance of coastal, juvenile-dominated habitats for green turtles, as well as the need for effective conservation and management strategies to safeguard them.
Orientia tsutsugamushi, the agent of scrub typhus

Orientia tsutsugamushi is a mite-borne bacterium belonging to the family Rickettsiaceae and is responsible for the disease scrub typhus in humans. It is an obligate intracellular parasite of trombiculid mites, in which natural transmission is maintained from the female to its eggs (transovarial transmission) and from the eggs to adults (transstadial transmission). With a genome of only 2.0–2.7 Mb, it has the most repeated DNA sequences among bacteria. It is transmitted by mite larvae (chiggers) from rodents, the natural hosts of mites, to humans through accidental bites. Naosuke Hayashi first described it in 1920, giving it the name Theileria tsutsugamushi, but it was renamed to Orientia tsutsugamushi in 1995, owing to its unique properties. Unlike other Gram-negative bacteria, its cell wall lacks lipophosphoglycan and peptidoglycan. It instead has a unique 56-kDa type-specific antigen (TSA56), which gives rise to many strains (sub-types) of the bacterium such as Karp, Gilliam, Kato, Shimokoshi, Kuroki, and Kawasaki. It is most closely related to Candidatus Orientia chuto, a species described in 2010. Primarily indicated by undifferentiated febrile illnesses, the infection can be complicated and often fatal. Diagnosis is difficult and requires laborious detection methods such as the Weil–Felix test, rapid immunochromatographic test, immunofluorescence assays, ELISA, or PCR. Eschar, if present on the skin, is a good diagnostic indicator. One million infections are estimated to occur annually in the endemic region called the Tsutsugamushi Triangle, which covers the Russian Far East in the north, Japan in the east, northern Australia in the south, and Afghanistan in the west. However, infections have also spread to Africa, Europe and South America. Antibiotics such as azithromycin and doxycycline are the main prescription drugs. There is no vaccine for the infection.
Aggregatibacter actinomycetemcomitans LtxA Hijacks Endocytic Trafficking Pathways in Human Lymphocytes

Leukotoxin (LtxA) from oral pathogen Aggregatibacter actinomycetemcomitans is a secreted membrane-damaging protein. LtxA is internalized by β2 integrin LFA-1 (CD11a/CD18) expressing leukocytes and ultimately causes cell death; however toxin localization in the host cell is poorly understood and these studies fill this void. We investigated LtxA trafficking using multi-fluor confocal imaging, flow cytometry and Rab5 knockdown in human T lymphocyte Jurkat cells. Planar lipid bilayers were used to characterize LtxA pore-forming activity at different pH. Our results demonstrate that LtxA/LFA-1 complex gains an access to the cytosol of Jurkat cells without evidence of plasma membrane damage utilizing dynamin-dependent and clathrin-independent mechanism. Upon internalization LtxA follows the LFA-1 endocytic trafficking pathways as identified by co-localization experiments with endosomal and lysosomal markers (Rab5, Rab11A, Rab7, and Lamp2) and CD11a. Knockdown of Rab5a resulted in loss of susceptibility of Jurkat cells to LtxA cytotoxicity suggesting that late events of LtxA endocytic trafficking are required for toxicity. The toxin trafficking via the degradation endocytic pathway may culminate in delivery of the protein to lysosomes or its accumulation in Rab11A-dependent recycling endosomes. The ability of LtxA to form pores at acidic pH may result in permeabilization of the endosomal and lysosomal membranes.
Safety and Effectiveness of De-escalated Radiation Dose in T1-3 Nasopharyngeal Carcinoma: A Propensity Matched Analysis

Backgrounds: With the excellent local control in T1 to T3 nasopharyngeal carcinoma (NPC) treated with intensity modulated radiotherapy (IMRT), the importance of toxicities is increasingly being recognised. This retrospective propensity score analysis sought to assess whether moderate dose reduction compromised long-term outcome compared with standard dose in T1-3 NPCs. Materials and Methods: A total of 266 patients (67 female, 199 male) with a median age of 50 years between June 2011 and June 2015 were analysed. All were treated with IMRT, with or without systemic chemotherapy. The prescription radiation dose to gross tumor is 70Gy/2.12Gy/33F in our institution. Results: With a median follow-up time of 50 months, the 5-year loco-regional failure-free survival (LRFS) and overall survival (OS) were 93.5% and 81.8%, respectively. 32 patients received radiation dose less than prescription dose, with a median dose of 63.6Gy (53-67Gy). Another 234 patients received exactly the prescription dose of 70Gy. Propensity scores were computed (32 patients treated with de-escalated dose and 64 patients with standard dose), there was no significant difference in 5-year LRFS and 5-year OS between the two groups (92.5% and 91.7% with standard dose; 82.1% and 85.7% with de-escalation dose; p=0.863 for LRFS and 0.869 for OS). No independent prognostic factor was associated with loco-regional failure in univariate analysis. Conclusions: T1-3 nasopharyngeal carcinoma presenting with superior locoregional control, a moderately reduced dose (about 10%) delivered with IMRT resulted in comparable prognosis to those with prescription dose of 70Gy.