Research of geotechnical properties of slope covers from Jamne and Jaszcze stream valleys in Gorce Mts.

W pracy przedstawione zostały wyniki badań parametrów geotechnicznych gruntów stanowiących pokrywy stokowe dwóch dolin potoków górskich w Gorcach w aspekcie oceny ich podatności osuwiskowej. Badania terenowe obejmowały określenie podstawowych właściwości fizycznych gruntów na kilku stanowiskach zlokalizowanych na zboczach obydwu dolin. Natomiast badania laboratoryjne obejmowały oznaczenie składu uziarnienia, granic konsystencji, współczynnika filtracji oraz wytrzymałości na ścinanie w aparacie bezpośredniego ścinania próbek zawodnionych oraz w aparacie trójosiowego ściskania metodą CIU. Wyniki badań wykazały, że badane grunty można określić jako utwory gruboziarniste z nieznaczną zawartością frakcji ilastej, charakteryzujące się niską plastycznością. Wartości kąta tarcia wewnętrznego większości badanych gruntów były wysokie i wahały się w zakresie od 28 do 38° , a spójności od 0 do 7 kPa. Generalnie większe wartości kąta tarcia wewnętrznego, a mniejsze spójności uzyskano z badań w aparacie trójosiowego ściskania. Współczynniki infiltracji z badań terenowych pozwalają scharakteryzować badane utwory jako średnio-przepuszczalne. Obliczenia stateczności wykonane z wykorzystaniem modelu SINMAP wykazały, że znaczna część analizowanego obszaru jest narażona na ruchy masowe, co daje bardziej konserwatywną oceną podatności osuwiskowej niż podają wyniki opracowane w programie SOPO. Z kolei probabilistyczna ocena stateczności wskazuje, że prawdopodobieństwo utraty stateczności wzrasta na zboczach o nachyleniu przekraczającym 20°, a uzyskane wyniki obliczeń pozwalają uzyskać bardziej szczegółowy obraz podatności rozpatrywanego obszaru na ruchy masowe niż uzyskano stosując model SINMAP.Test results of geotechnical parameters of slope covers from valleys of two mountainous streams from Gorce Mts. are presented in the paper. The tests were carried out in the context of estimation of slope stability of analyzed watersheds. Field studies included determination of basic soil physical properties at several sites within studied area, laboratory tests involved determination of particle size distribution, consistency limits, permeability coefficients and shear strengths, which were carried out at direct shear box and CIU tests in triaxial apparatus. Test results revealed that tested slope covers can be described as coarse-grained soils with low content clay fraction, characterized by low plasticity. The values of the internal friction angle of the average bad land were high and ranged from 28 to 38 degrees, whereas cohesion varied from 0 to 7 kPa. Generally higher values of angle of internal friction and lower cohesion were obtained from triaxial tests. Values of permeability coefficients determined using infiltration method allow to characterize tested soils as a semi-permeable medium. Stability calculations using the SINMAP model have shown that a significant part of the analyzed area is prone to mass movements, giving a more conservative assessment of landslide vulnerability than results of the SOPO report. The likelihood of slope failure increases significantly on slopes of inclination exceeding 20 degrees, and the results of the calculations obtained the method provide a more detailed information of the mass movements susceptibility of the area than were obtained using the SINMAP model

Induction of synchronized estrus in dairy goats with different gonadotrophins.

The objective of this study was to evaluate lhe efficiency of two gonadotrophins in induction of estrus in dairy goats. A total of 47 dairy goats were randomly divided according to breed into two treatments (T1 and T2). In both treatments, goats received intravaginal sponges containing 60 mg medroxy-progesterone acetate for six days and sub- vulvar administration of 22.5 mg of d-cloprostenol at the time of sponge insertion. In TI (n=23) and T2 (n=24), animaIs received intramuscuIar administration of 200 lU and 250 lU of eCG and hCG, respectively. After sponge removal, goats were monitored twice daily (06:00 a.m. and 18:00 p.m.) with bucks. Animals were bred at lhe start of estrus and at each 12 hours interval until lhe end of estrus. Pregnancy was checked by ultrasonography 63 days after breeding. Percentage of animals in estrus did not differ (P>0.05) between TI (95.6%) and T2 (78.3%). There was no effect (P>0.05) of treatment on interval from sponge removal to lhe Start of estrus (IE) and duration of estrus (DE). The" average IE was 48.0 + 9.4h and 46.2+ 8.4h for eCG and hCG, respectively. The average DE was 20.7 + 11.9h and 18.8 + 9.0h for eCG and hCG, respectively. Pregnancy cate did not differ (P>0.05) between eCG (77.3%) and hCG (61.1%). Results of this study showed that estrus can be efficiently induced in female goats outside lhe breeding season with both eCG and hCG

Analysis of meiotic recombination in 22q11.2, a region that frequently undergoes deletions and duplications

BACKGROUND: The 22q11.2 deletion syndrome is the most frequent genomic disorder with an estimated frequency of 1/4000 live births. The majority of patients (90%) have the same deletion of 3 Mb (Typically Deleted Region, TDR) that results from aberrant recombination at meiosis between region specific low-copy repeats (LCRs). METHODS: As a first step towards the characterization of recombination rates and breakpoints within the 22q11.2 region we have constructed a high resolution recombination breakpoint map based on pedigree analysis and a population-based historical recombination map based on LD analysis. RESULTS: Our pedigree map allows the location of recombination breakpoints with a high resolution (potential recombination hotspots), and this approach has led to the identification of 5 breakpoint segments of 50 kb or less (8.6 kb the smallest), that coincide with historical hotspots. It has been suggested that aberrant recombination leading to deletion (and duplication) is caused by low rates of Allelic Homologous Recombination (AHR) within the affected region. However, recombination rate estimates for 22q11.2 region show that neither average recombination rates in the 22q11.2 region or within LCR22-2 (the LCR implicated in most deletions and duplications), are significantly below chromosome 22 averages. Furthermore, LCR22-2, the repeat most frequently implicated in rearrangements, is also the LCR22 with the highest levels of AHR. In addition, we find recombination events in the 22q11.2 region to cluster within families. Within this context, the same chromosome recombines twice in one family; first by AHR and in the next generation by NAHR resulting in an individual affected with the del22q11.2 syndrome. CONCLUSION: We show in the context of a first high resolution pedigree map of the 22q11.2 region that NAHR within LCR22 leading to duplications and deletions cannot be explained exclusively under a hypothesis of low AHR rates. In addition, we find that AHR recombination events cluster within families. If normal and aberrant recombination are mechanistically related, the fact that LCR22s undergo frequent AHR and that we find familial differences in recombination rates within the 22q11.2 region would have obvious health-related implications

Novel phages of healthy skin metaviromes from South Africa

Recent skin metagenomic studies have investigated the harbored viral diversity and its possible influence on healthy skin microbial populations, and tried to establish global patterns of skin-phage evolution. However, the detail associated with the phages that potentially play a role in skin health has not been investigated. While skin metagenome and -metavirome studies have indicated that the skin virome is highly site specific and shows marked interpersonal variation, they have not assessed the presence/absence of individual phages. Here, we took a semi-culture independent approach (metaviromic) to better understand the composition of phage communities on skin from South African study participants. Our data set adds over 130 new phage species of the skin to existing databases. We demonstrated that identical phages were present on different individuals and in different body sites, and we conducted a detailed analysis of the structural organization of these phages. We further found that a bacteriophage related to the Staphylococcus capitis phage Stb20 may be a common skin commensal virus potentially regulating its host and its activities on the ski

Neisseria gonorrhoeae sequence typing for antimicrobial resistance, a novel antimicrobial resistance multilocus typing scheme for tracking global dissemination of N. Gonorrhoeae strains

A curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants in Neisseria gonorrhoeae was developed and is publicly accessible (https://ngstar.Canada.ca). The N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes (penA, mtrR, porB, ponA, gyrA, parC, and 23S rRNA) associated with resistance to β-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entire penA sequence, combining the historical nomenclature for penA types I to XXXVIII with novel nucleotide sequence designations; the full mtrR sequence and a portion of its promoter region; portions of ponA, porB, gyrA, and parC; and 23S rRNA sequences. NG-STAR grouped 768 isolates into 139 sequence types (STs) (n = 660) consisting of 29 clonal complexes (CCs) having a maximum of a single-locus variation, and 76 NG-STAR STs (n = 109) were identified as unrelated singletons. NG-STAR had a high Simpson's diversity index value of 96.5% (95% confidence interval [CI] = 0.959 to 0.969). The most common STs were NG-STAR ST-90 (n = 100; 13.0%), ST-42 and ST-91 (n = 45; 5.9%), ST-64 (n = 44; 5.72%), and ST-139 (n = 42; 5.5%). Decreased susceptibility to azithromycin was associated with NGSTAR ST-58, ST-61, ST-64, ST-79, ST-91, and ST-139 (n = 156; 92.3%); decreased susceptibility to cephalosporins was associated with NG-STAR ST-90, ST-91, and ST-97 (n = 162; 94.2%); and ciprofloxacin resistance was associated with NG-STAR ST-26, ST-90, ST-91, ST-97, ST-150, and ST-158 (n = 196; 98.0%). All isolates of NG-STAR ST- 42, ST-43, ST-63, ST-81, and ST-160 (n = 106) were susceptible to all four antimicrobials. The standardization of nomenclature associated with antimicrobial resistance determinants through an internationally available database will facilitate the monitoring of the global dissemination of antimicrobial-resistant N. gonorrhoeae strains

A proposed new bacteriophage subfamily: “Jerseyvirinae”

© 2015, Springer-Verlag Wien. Based on morphology and comparative nucleotide and protein sequence analysis, a new subfamily of the family Siphoviridae is proposed, named “Jerseyvirinae” and consisting of three genera, “Jerseylikevirus”, “Sp3unalikevirus” and “K1glikevirus”. To date, this subfamily consists of 18 phages for which the genomes have been sequenced. Salmonella phages Jersey, vB_SenS_AG11, vB_SenS-Ent1, vB_SenS-Ent2, vB_SenS-Ent3, FSL SP-101, SETP3, SETP7, SETP13, SE2, SS3e and wksl3 form the proposed genus “Jerseylikevirus”. The proposed genus “K1glikevirus” consists of Escherichia phages K1G, K1H, K1ind1, K1ind2 and K1ind3. The proposed genus “Sp3unalikevirus” contains one member so far. Jersey-like phages appear to be widely distributed, as the above phages were isolated in the UK, Canada, the USA and South Korea between 1970 and the present day. The distinguishing features of this subfamily include a distinct siphovirus morphotype, genomes of 40.7-43.6kb (49.6-51.4mol% G+C), a syntenic genome organisation, and a high degree of nucleotide sequence identity and shared proteins. All known members of the proposed subfamily are strictly lytic

Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium.

BACKGROUND The Invasive Respiratory Infection Surveillance (IRIS) Consortium was established to assess the impact of the COVID-19 pandemic on invasive diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Streptococcus agalactiae. We aimed to analyse the incidence and distribution of these diseases during the first 2 years of the COVID-19 pandemic compared to the 2 years preceding the pandemic. METHODS For this prospective analysis, laboratories in 30 countries and territories representing five continents submitted surveillance data from Jan 1, 2018, to Jan 2, 2022, to private projects within databases in PubMLST. The impact of COVID-19 containment measures on the overall number of cases was analysed, and changes in disease distributions by patient age and serotype or group were examined. Interrupted time-series analyses were done to quantify the impact of pandemic response measures and their relaxation on disease rates, and autoregressive integrated moving average models were used to estimate effect sizes and forecast counterfactual trends by hemisphere. FINDINGS Overall, 116 841 cases were analysed: 76 481 in 2018-19, before the pandemic, and 40 360 in 2020-21, during the pandemic. During the pandemic there was a significant reduction in the risk of disease caused by S pneumoniae (risk ratio 0·47; 95% CI 0·40-0·55), H influenzae (0·51; 0·40-0·66) and N meningitidis (0·26; 0·21-0·31), while no significant changes were observed for S agalactiae (1·02; 0·75-1·40), which is not transmitted via the respiratory route. No major changes in the distribution of cases were observed when stratified by patient age or serotype or group. An estimated 36 289 (95% prediction interval 17 145-55 434) cases of invasive bacterial disease were averted during the first 2 years of the pandemic among IRIS-participating countries and territories. INTERPRETATION COVID-19 containment measures were associated with a sustained decrease in the incidence of invasive disease caused by S pneumoniae, H influenzae, and N meningitidis during the first 2 years of the pandemic, but cases began to increase in some countries towards the end of 2021 as pandemic restrictions were lifted. These IRIS data provide a better understanding of microbial transmission, will inform vaccine development and implementation, and can contribute to health-care service planning and provision of policies. FUNDING Wellcome Trust, NIHR Oxford Biomedical Research Centre, Spanish Ministry of Science and Innovation, Korea Disease Control and Prevention Agency, Torsten Söderberg Foundation, Stockholm County Council, Swedish Research Council, German Federal Ministry of Health, Robert Koch Institute, Pfizer, Merck, and the Greek National Public Health Organization

Prophage exotoxins enhance colonization fitness in epidemic scarlet fever-causing Streptococcus pyogenes

Abstract: The re-emergence of scarlet fever poses a new global public health threat. The capacity of North-East Asian serotype M12 (emm12) Streptococcus pyogenes (group A Streptococcus, GAS) to cause scarlet fever has been linked epidemiologically to the presence of novel prophages, including prophage ΦHKU.vir encoding the secreted superantigens SSA and SpeC and the DNase Spd1. Here, we report the molecular characterization of ΦHKU.vir-encoded exotoxins. We demonstrate that streptolysin O (SLO)-induced glutathione efflux from host cellular stores is a previously unappreciated GAS virulence mechanism that promotes SSA release and activity, representing the first description of a thiol-activated bacterial superantigen. Spd1 is required for resistance to neutrophil killing. Investigating single, double and triple isogenic knockout mutants of the ΦHKU.vir-encoded exotoxins, we find that SpeC and Spd1 act synergistically to facilitate nasopharyngeal colonization in a mouse model. These results offer insight into the pathogenesis of scarlet fever-causing GAS mediated by prophage ΦHKU.vir exotoxins

Serotype distribution of Streptococcus pneumoniae causing invasive disease in children in the post-PCV era:A systematic review and meta-analysis

BACKGROUND:Routine immunisation with pneumococcal conjugate vaccines (PCV7/10/13) has reduced invasive pneumococcal disease (IPD) due to vaccine serotypes significantly. However, an increase in disease due to non-vaccine types, or serotype replacement, has been observed. Serotypes' individual contributions to IPD play a critical role in determining the overall effects of PCVs. This study examines the distribution of pneumococcal serotypes in children to identify leading serotypes associated with IPD post-PCV introduction. METHODS:A systematic search was performed to identify studies and surveillance reports (published between 2000 and December 2015) of pneumococcal serotypes causing childhood IPD post-PCV introduction. Serotype data were differentiated based on the PCV administered during the study period: PCV7 or higher valent PCVs (PCV10 or PCV13). Meta-analysis was conducted to estimate the proportional contributions of the most frequent serotypes in childhood IPD in each period. RESULTS:We identified 68 studies reporting serotype data among IPD cases in children. We analysed data from 38 studies (14 countries) where PCV7 was administered and 20 (24 countries) where PCV10 or PCV13 have been introduced. Studies reported early and late periods of PCV7 administration (range: 2001∓13). In these settings, serotype 19A was the most predominant cause of childhood IPD, accounting for 21.8% (95%CI 18.6∓25.6) of cases. In countries that have introduced higher valent PCVs, study periods were largely representative of the transition and early years of PCV10 or PCV13. In these studies, the overall serotype-specific contribution of 19A was lower (14.2% 95%CI 11.1∓18.3). Overall, non-PCV13 serotypes contributed to 42.2% (95%CI 36.1∓49.5%) of childhood IPD cases. However, regional differences were noted (57.8% in North America, 71.9% in Europe, 45.9% in Western Pacific, 28.5% in Latin America, 42.7% in one African country, and 9.2% in one Eastern Mediterranean country). Predominant non-PCV13 serotypes overall were 22F, 12F, 33F, 24F, 15C, 15B, 23B, 10A, and 38 (descending order), but their rank order varied by region. CONCLUSION:Childhood IPD is associated with a wide number of serotypes. In the early years after introduction of higher valent PCVs, non-PCV13 types caused a considerable proportion of childhood IPD. Serotype data, particularly from resource-limited countries with high burden of IPD, are needed to assess the importance of serotypes in different settings. The geographic diversity of pneumococcal serotypes highlights the importance of continued surveillance to guide vaccine design and recommendations