Environmental factors shaping the gut microbiome in a Dutch population.

The gut microbiome is associated with diverse diseases1-3, but a universal signature of a healthy or unhealthy microbiome has not been identified, and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. Here we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We correlated these to 241 host and environmental factors, including physical and mental health, use of medication, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is shaped primarily by the environment and cohabitation. Only around 6.6% of taxa are heritable, whereas the variance of around 48.6% of taxa is significantly explained by cohabitation. By identifying 2,856 associations between the microbiome and health, we find that seemingly unrelated diseases share a common microbiome signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, with numerous early-life and current factors being significantly associated with microbiome function and composition. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.

Origin of Magnetism in a Supposedly Nonmagnetic Osmium Oxide.

A supposedly nonmagnetic 5d^{1} double perovskite oxide is investigated by a combination of spectroscopic and theoretical methods, namely, resonant inelastic x-ray scattering, x-ray absorption spectroscopy, magnetic circular dichroism, and multiplet ligand-field calculations. We found that the large spin-orbit coupling admixes the 5d t_{2g} and e_{g} orbitals, covalency raises the 5d population well above the nominal value, and the local symmetry is lower than O_{h}. The obtained electronic interactions account for the finite magnetic moment of Os in this compound and, in general, of 5d^{1} ions. Our results provide direct evidence of elusive Jahn-Teller distortions, hinting at a strong electron-lattice coupling.

Optically excited structural transition in atomic wires on surfaces at the quantum limit.

Transient control over the atomic potential-energy landscapes of solids could lead to new states of matter and to quantum control of nuclear motion on the timescale of lattice vibrations. Recently developed ultrafast time-resolved diffraction techniques combine ultrafast temporal manipulation with atomic-scale spatial resolution and femtosecond temporal resolution. These advances have enabled investigations of photo-induced structural changes in bulk solids that often occur on timescales as short as a few hundred femtoseconds. In contrast, experiments at surfaces and on single atomic layers such as graphene report timescales of structural changes that are orders of magnitude longer. This raises the question of whether the structural response of low-dimensional materials to femtosecond laser excitation is, in general, limited. Here we show that a photo-induced transition from the low- to high-symmetry state of a charge density wave in atomic indium (In) wires supported by a silicon (Si) surface takes place within 350 femtoseconds. The optical excitation breaks and creates In-In bonds, leading to the non-thermal excitation of soft phonon modes, and drives the structural transition in the limit of critically damped nuclear motion through coupling of these soft phonon modes to a manifold of surface and interface phonons that arise from the symmetry breaking at the silicon surface. This finding demonstrates that carefully tuned electronic excitations can create non-equilibrium potential energy surfaces that drive structural dynamics at interfaces in the quantum limit (that is, in a regime in which the nuclear motion is directed and deterministic). This technique could potentially be used to tune the dynamic response of a solid to optical excitation, and has widespread potential application, for example in ultrafast detectors.

Surface Resonant Raman Scattering from Cu(110).

We report the first evidence of Raman scattering from surface phonons of a pristine metal surface. Our study reveals a Raman-active surface vibrational resonance on Cu(110) with a surprisingly large scattering efficiency. With the incident photon energy close to the energy of the Cu(110) surface state electronic transition, the Raman scattering from the surface optical resonance can be significantly enhanced, while any contribution from bulk phonons is absent.

Comparative characterisation of human and ovine non-aureus staphylococci isolated in Sardinia (Italy) for antimicrobial susceptibility profiles and resistance genes.

We present the comparative characterisation of 195 non-aureus staphylococci (NAS) isolates obtained from sheep (n = 125) and humans (n = 70) in Sardinia, Italy, identified at the species level by gap gene polymerase chain reaction (PCR) followed by restriction fragment length polymorphism analysis with AluI. Isolates were tested phenotypically with a disc diffusion method and genotypically by PCR, for resistance to 11 antimicrobial agents including cationic antiseptic agents. Among the ovine isolates, Staphylococcus epidermidis (n = 57), S. chromogenes (n = 29), S. haemolyticus (n = 17), S. simulans (n = 8) and S. caprae (n = 6) were the most prevalent species, while among human isolates, S. haemolyticus (n = 28) and S. epidermidis (n = 26) were predominant, followed by S. lugdunensis and S. hominis (n = 4). Of the 125 ovine isolates, 79 (63.2%) did not carry any of the resistance genes tested, while the remainder carried resistance genes for at least one antibiotic. The highest resistance rates among ovine isolates were recorded against tetracycline (20.8%), and penicillin (15.2%); none was resistant to methicillin and two exhibited multidrug resistance (MDR); one of which was positive for the antiseptic resistance smr gene. By contrast, most human isolates (59/70, 84.3%) were resistant to ⩾1 antimicrobials, and 41 (58.6%) were MDR. All 52 (74.3%) penicillin-resistant isolates possessed the blaZ gene, and 33 of 70 (47.1%) harboured the mec gene; of these, seven were characterised by the Staphylococcal Chromosomal Cassette (SCCmec) type IV, 6 the type V, 5 of type III and one representative each of type I and type II. The majority (57.1%) was erythromycin-resistant and 17 isolates carried only the efflux msrA gene, 11 the methylase ermC gene and an equal number harboured both of the latter genes. Moreover, 23 (32.8%) were tetracycline-resistant and all but one possessed only the efflux tetK gene. qacA/B and smr genes were detected in 27 (38.6%) and 18 (25.7%) human NAS, respectively. These results underline a marked difference in species distribution and antimicrobial resistance between ovine and human-derived NAS.

Vibration-Driven Self-Doping of Dangling-Bond Wires on Si(553)-Au Surfaces.

Density-functional theory is used to explore the Si(553)-Au surface dynamics. Our study (i) reveals a complex two-stage order-disorder phase transition where with rising temperature first the ×3 order along the Si step edges and, subsequently, the ×2 order of the Au chains is lost, (ii) identifies the transient modification of the electron chemical potential during soft Au chain vibrations as instrumental for disorder at the step edge, and (iii) shows that the transition leads to a self-doping of the Si dangling-bond wire at the step edge. The calculations are corroborated by Raman measurements of surface phonon modes and explain previous electron diffraction, scanning tunneling microscopy, and surface transport data.

Does antithrombotic prophylaxis worsen early outcomes of total thyroidectomy? - a retrospective cohort study.

BACKGROUND: Currently, there is no strong evidence on the effectiveness and safety of pharmacological antithrombotic prophylaxis in thyroid surgery. The aim of this study was to establish whether the prophylactic use of low-molecular-weight heparin (LMWH) could negatively affect the early outcomes of patients undergoing total thyroidectomy. METHODS: Data from patients submitted to total thyroidectomy between February 2013 and October 2017 were retrospectively collected and analysed. Only patients with indication to antithrombotic prophylaxis according to current guidelines were included in the study. Eligible cases were divided into two groups, which corresponded to two distinct periods of our surgical practice: Group A, which included 178 consecutive patients who were submitted to antithrombotic prophylaxis with LMWH, and Group B, which included 348 consecutive patients who did not receive prophylaxis. Primary endpoints were the incidence of post-operative cervical haematomas (POCH) and thromboembolic events. Secondary endpoint was the length of postoperative hospital stay. Statistical analysis was performed by using Student's t test for continuous variables and Chi-square test for categorical variables. A P value of less than 0.05 was considered statistically significant. RESULTS: The two groups of patients were comparable in terms of age, gender, thyroid disease, duration of surgery, and weight of the thyroid gland. Overall, no thromboembolic events were registered. The comparative analysis of the other outcome measures, showed no significant differences between the two groups (POCH: 2 cases (1.12%) in Group A vs 8 cases (2.30%) in Group B - p 0.349; Postoperative hospital stay: 2.90 ± 0.86 days in Group A vs 2.89 ± 0.99 days in Group B - p 0.908). CONCLUSIONS: Data from this study do not support or contraindicate the use of antithrombotic prophylaxis in thyroid surgery. However, since thyroidectomy is a closed-space procedure, and even modest bleeding may quickly result in airway compression and death by asphyxia, mechanical prophylaxis should be preferred to LMWH whenever possible. TRIAL REGISTRATION: ISRCTN ISRCTN12029395. Registered 05/02/2018 retrospectively registered.

Population-based analysis of hospitalizations in a West-European region revealed major changes in hospital utilization for patients with systemic lupus erythematosus over the period 2001-2012.

OBJECTIVE: The objective of this paper is to evaluate hospital admissions in systemic lupus erythematosus (SLE) patients through a retrospective population-based study analyzing hospitalization data during 2001-2012 in Sardinia, an Italian region with universal health system coverage. METHODS: Data on the hospital discharge records with the ICD-9-CM code for SLE (710.0) were obtained from the Department of Health and Hygiene and analyzed, mostly focusing on primary and non-primary diagnosis and Diagnosis-Related Group (DRG) code. In order to establish the significance of the annual trend for number and type of primary and non-primary discharge diagnosis, the two-tailed Cochran-Armitage test for trend was applied. In order to estimate SLE prevalence, data from administrative database and medical records were assembled. RESULTS: This study included 6222 hospitalizations in 1675 patients (87% women). Hospitalizations with SLE as primary diagnosis were 3782 (58.0%) and significantly decreased during the study period. The annual number of renal, hematologic and neuropsychiatric disorders as non-primary diagnosis associated with SLE remained constant; however, their percentage increased (p < 0.0001) because of a declining number of admissions for SLE without associated diagnosis and without complications. Hospitalizations with SLE as non-primary diagnosis showed a significant upward trend in number and percentage of cerebrovascular accident (p = 0.0004), acute coronary syndrome (p = 0.0004) and chronic renal failure (p = 0.0003) as underlying primary diagnosis, while complications of pregnancy, labor and childbirth (p = 0.3375), malignancies (p = 0.6608) and adverse drug reactions (p = 0.2456) did not show statistically significant changes. Infections showed an increasing trend between 2001 and 2012 but did not reach statistical significance (p = 0.0304). After correction for hospitalization (93.8%) and survival (91.1%) rates calculated over the study period, the 2012 SLE prevalence in Sardinia was estimated to be 99.3 per 100,000 inhabitants. CONCLUSIONS: While overall hospitalizations for SLE patients declined, those for cerebrovascular accident, acute coronary syndrome and chronic renal failure as underlying primary diagnosis increased during the study period.

Mutual Independence of Critical Temperature and Superfluid Density under Pressure in Optimally Electron-Doped Superconducting LaFeAsO(1-x)F(x).

The superconducting properties of LaFeAsO(1-x)F(x) under conditions of optimal electron doping are investigated upon the application of external pressure up to ∼23 kbar. Measurements of muon-spin spectroscopy and dc magnetometry evidence a clear mutual independence between the critical temperature T(c) and the low-temperature saturation value for the ratio n(s)/m(*) (superfluid density over effective band mass of Cooper pairs). Remarkably, a dramatic increase of ∼30% is reported for n(s)/m(*) at the maximum pressure value while T(c) is substantially unaffected in the whole accessed experimental window. We argue and demonstrate that the explanation for the observed results must take the effect of nonmagnetic impurities on multiband superconductivity into account. In particular, the unique possibility to modify the ratio between intraband and interband scattering rates by acting on structural parameters while keeping the amount of chemical disorder constant is a striking result of our proposed model.

Routine use of a protease zymogen-based colorimetric assay for the detection of Beta-glucan and its role in clinical practice.

The detection of Aspergillus antigen (galactomannan) is considered a reliable marker for the diagnosis of invasive aspergillosis (IA), yet the sensibility and specificity of the assays commonly employed in routine are not optimal. The aim of the present study was to investigate whether the detection of another panfungal antigen, the (1,3)-b-D-glucan could have an auxiliary role in the identification of patients with IA. The study was carried out on 63 sera belonging to patients who had been screened for galactomannan, according to the clinical suspect of IA. Our data show that the positive galactomannan results were not confirmed by positive (1,3)-b-D-glucan results in patients receiving therapy with beta-lactam antibiotics associated with tazobactam, whereas in all the other cases, with the exception of four, the results of the (1,3)-b-D-glucan test were confirmatory of the galactomannan results.

It could suddenly happen: delayed rupture of the trachea after total thyroidectomy. A case report.

INTRODUCTION: We report the case of a patient who presented with subcutaneous emphysema, dyspnea and cough 7 days after total thyroidectomy for cancer. In addition we review the Literature and discuss the therapeutic challenges as well as management options. CASE REPORT: A 17-year old female patient underwent a total thyroidectomy with right cervical lymph adenectomy for papillar cancer. Lung metastases are present. On postoperative day 7 she presented with face and neck swelling due to subcutaneous emphysema, dyspnea and persistent cough. The radiological evaluation revealed a tear on the right antero-lateral wall of the trachea. The patient underwent surgical exploration of the neck which confirmed the tracheal rupture and showed an important tracheal necrosis all around the tear. Due to the impossibility to make primary closure of the trachea or a tracheal resection, the tear was repaired with muscular flap interposition, (around the trachea as a scarf ), using the contralateral clavicular part of sternocleidomastoid muscle and prethyroid muscles bilaterally. The postoperative course was uneventful and the patient is alive 20 months after surgery and iodine induced adjuvant therapy. CONCLUSION: Delayed tracheal rupture should be suspected in all patients who present subcutaneous emphysema after thyroid surgery. The lesion should be promptly treated with primary closure or tracheal resection when possible. Muscular flap interposition could be a safe alternative option when the other procedures are contraindicated.

Depth-dependent study of time-reversal symmetry-breaking in the kagome superconductor AV3Sb5.

The breaking of time-reversal symmetry (TRS) in the normal state of kagome superconductors AV3Sb5 stands out as a significant feature, but its tunability is unexplored. Using low-energy muon spin rotation and local field numerical analysis, we study TRS breaking as a function of depth in single crystals of RbV3Sb5 (with charge order) and Cs(V0.86Ta0.14)3Sb5 (without charge order). In the bulk of RbV3Sb5 (>33 nm from the surface), we observed an increase in the internal magnetic field width in the charge-ordered state. Near the surface (<33 nm), the muon spin relaxation rate is significantly enhanced and this effect commences at temperatures significantly higher than the onset of charge order. In contrast, no similar field width enhancement was detected in Cs(V0.86Ta0.14)3Sb5, either in the bulk or near the surface. These observations indicate a strong connection between charge order and TRS breaking and suggest that TRS breaking can occur prior to long-range charge order.

A trans-specific polymorphism in ZC3HAV1 is maintained by long-standing balancing selection and may confer susceptibility to multiple sclerosis.

The human ZC3HAV1 gene encodes an antiviral protein. The longest splicing isoform of ZC3HAV1 contains a C-terminal PARP-like domain, which has evolved under positive selection in primates. We analyzed the evolutionary history of this same domain in humans and in Pan troglodytes. We identified two variants that segregate in both humans and chimpanzees; one of them (rs3735007) does not occur at a hypermutable site and accounts for a nonsynonymous substitution (Thr851Ile). The probability that the two trans-specific polymorphisms have occurred independently in the two lineages was estimated to be low (P = 0.0054), suggesting that at least one of them has arisen before speciation and has been maintained by selection. Population genetic analyses in humans indicated that the region surrounding the shared variants displays strong evidences of long-standing balancing selection. Selection signatures were also observed in a chimpanzee population sample. Inspection of 1000 Genomes data confirmed these findings but indicated that search for selection signatures using low-coverage whole-genome data may need masking of repetitive sequences. A case-control study of more than 1,000 individuals from mainland Italy indicated that the Thr851Ile SNP is significantly associated with susceptibility to multiple sclerosis (MS) (odds ratio [OR] = 1.47, 95% confidence intervals [CI]: 1.08-1.99, P = 0.011). This finding was confirmed in a larger sample of 4,416 Sardinians cases/controls (OR = 1.18, 95% CI: 1.037-1.344, P = 0.011), but not in a population from Belgium. We provide one of the first instances of human/chimpanzee trans-specific coding variant located outside the major histocompatibility complex region. The selective pressure is likely to be virus driven; in modern populations, this variant associates with susceptibility to MS, possibly via the interaction with environmental factors.

Meta-analysis of genome-wide association studies for personality.

Personality can be thought of as a set of characteristics that influence people's thoughts, feelings and behavior across a variety of settings. Variation in personality is predictive of many outcomes in life, including mental health. Here we report on a meta-analysis of genome-wide association (GWA) data for personality in 10 discovery samples (17,375 adults) and five in silico replication samples (3294 adults). All participants were of European ancestry. Personality scores for Neuroticism, Extraversion, Openness to Experience, Agreeableness and Conscientiousness were based on the NEO Five-Factor Inventory. Genotype data of ≈ 2.4M single-nucleotide polymorphisms (SNPs; directly typed and imputed using HapMap data) were available. In the discovery samples, classical association analyses were performed under an additive model followed by meta-analysis using the weighted inverse variance method. Results showed genome-wide significance for Openness to Experience near the RASA1 gene on 5q14.3 (rs1477268 and rs2032794, P=2.8 × 10(-8) and 3.1 × 10(-8)) and for Conscientiousness in the brain-expressed KATNAL2 gene on 18q21.1 (rs2576037, P=4.9 × 10(-8)). We further conducted a gene-based test that confirmed the association of KATNAL2 to Conscientiousness. In silico replication did not, however, show significant associations of the top SNPs with Openness and Conscientiousness, although the direction of effect of the KATNAL2 SNP on Conscientiousness was consistent in all replication samples. Larger scale GWA studies and alternative approaches are required for confirmation of KATNAL2 as a novel gene affecting Conscientiousness.

Surgical results and survival of older patients with unsuspected N2 (stage IIIA) non-small cell lung cancer.

PURPOSES: The optimal treatment of N2 non-small cell lung cancer (NSCLC) in older patients is still debate and represent an important treatment and ethical problem. PATIENTS AND METHODS: Between January 2000 to December 2010, 273 older patients underwent lung resection for (NSCLC). RESULTS: The overall-operative mortality was 9.5%. Risk factors for in-hospital mortality were pneumonectomy and poli-vasculopathy. One, 3 and 5-year survival were 73%, 23% and 16% respectively. CONCLUSIONS: In potentially operable older patients with NSCLC we need to make every effort to exclude N2 involvement because very poor long-term survival. Pneumonectomy in older patients gains prohibitive in-hospital mortality.

Is there a dose-response relationship of metformin treatment in patients with polycystic ovary syndrome? Results from a multicentric study.

STUDY QUESTION: Do different dosages of metformin account for different clinical and biochemical outcomes in women with polycystic ovary syndrome (PCOS) and do basal anthropometric and metabolic characteristics of the patients provide any indications regarding the dose required to reach the target effect? SUMMARY ANSWER: Different doses of metformin exerted the same effects on clinical, biochemical and metabolic parameters in patients affected by PCOS. WHAT IS KNOWN AND WHAT THIS PAPER ADDS: Since the insulin-sensitizing agents came into use in the management of PCOS, metformin has shown a positive benefits-risks ratio. Nonetheless, therapeutic schedules are not well standardized. This is the first study which systematically analyses the effect of different doses of metformin on clinical, hormonal and metabolic features of PCOS. On the basis of our results, higher doses are no more effective than lower doses. DESIGN: A multicentric cohort prospective study. A total of 250 PCOS women were enrolled, 49 lost to follow-up. Menstrual cyclicity, hormonal assays, oral glucose tolerance test, lipid profile and ultrasonographic pelvic examination were evaluated at the baseline and after 6 months of metformin treatment at different doses (1000, 1500 and 1700 mg). PARTICIPANTS AND SETTING: A total of 201 PCOS patients completed the study without protocol violations in three university hospitals: seventy-three patients from Centre A (treated with metformin 500 mg twice a day), 60 patients from Centre B (treated with metformin 500 mg three times a day) and 68 patients from Centre C (treated with metformin 850 mg twice a day). MAIN RESULTS AND THE ROLE OF CHANCE: Metformin exerted an overall positive effect on the clinical and endocrine-metabolic features of PCOS. The degree of these effects was independent of the administered dosage in every range of basal body mass index (BMI). When patients were stratified according to their insulinaemic status, scattered inter-doses differences were found in some of the outcome measures. Patients who exhibited an increase of >2 menstrual cycles/year were considered as responders to treatment. Responders had a higher basal BMI than non-responders and showed a greater reduction in plasma testosterone levels after metformin treatment, but other outcome measures did not differ significantly. Total insulin secretion in the 180 min following the glucose tolerance test before metformin treatment (basal AUC-I) was significantly correlated with the decrease in insulin secretion induced by metformin in both the whole group and in responders, but only correlated with the variation in the number of cycles in responders. BIAS, CONFOUNDING AND OTHER REASONS FOR CAUTION: The different doses were administered in different centres, and between-centre variation is a potential confounding factor. GENERALIZABILITY TO OTHER POPULATIONS: The paradigm of using the minimum effective dose of metformin could be pursued in other pathological conditions characterized by insulin resistance. STUDY FUNDING/COMPETING INTEREST(S): No funding or competing interests to declare.

Correlated trends of coexisting magnetism and superconductivity in optimally electron-doped oxypnictides.

We report on the recovery of the short-range static magnetic order and on the concomitant degradation of the superconducting state in optimally F-doped SmFe(1-x)Ru(x)AsO(0.85)F(0.15) for 0.1≤x≲0.5. The two reduced order parameters coexist within nanometer-size domains in the FeAs layers and eventually disappear around a common critical threshold x(c)~0.6. Superconductivity and magnetism are shown to be closely related to two distinct well-defined local electronic environments of the FeAs layers. The two transition temperatures, controlled by the isoelectronic and diamagnetic Ru substitution, scale with the volume fraction of the corresponding environments. This fact indicates that superconductivity is assisted by magnetic fluctuations, which are frozen whenever a short-range static order appears, and totally vanish above the magnetic dilution threshold x(c).