Miracle-dz/UniFAR-FTUs huggingface dataset:
Leucobacter aerolatus sp. nov., from the air of a duck barn.

A Gram-positive, non-spore-forming actinobacterium (Sj 10(T)) was isolated on tryptone soy agar from the air of a duck barn after filter sampling. Based on 16S rRNA gene sequence similarity studies, strain Sj 10(T) was shown to belong to the genus Leucobacter and was closely related to Leucobacter chromiireducens subsp. chromiireducens L-1(T) (97.8 %), Leucobacter tardus DSM 19811(T) (97.3 %) and Leucobacter luti RF6(T) (97.3 %). The peptidoglycan of strain Sj 10(T) contained 2,4-diaminobutyric acid in combination with a lower amount of lysine as diagnostic diamino acids. In addition, threonine, glycine, alanine and glutamic acid were found. Menaquinone MK-11 was the major respiratory quinone; MK-12 and MK-10 were detected in minor amounts. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol and one unknown component each of a phospholipid, glycolipid and aminoglycolipid. Strain Sj 10(T) contained the major fatty acids anteiso-C(15 : 0), iso-C(16 : 0) and anteiso-C(17 : 0), like other members of the genus Leucobacter. Results of DNA-DNA hybridization, physiological and biochemical tests enabled strain Sj 10(T) to be differentiated genotypically and phenotypically from the most closely related Leucobacter species. Strain Sj 10(T) represents a novel species of the genus Leucobacter, for which the name Leucobacter aerolatus sp. nov. is proposed, with Sj 10(T) (=DSM 22806(T) =CCM 7705(T)) as the type strain.
A prospective randomized comparison of traditional laparoendoscopic single-site surgery with needlescopic-assisted laparoscopic nephrectomy in the porcine model.

BACKGROUND AND PURPOSE Laparoendoscopic single-site (LESS) surgery produces virtually no scar but is technically challenging because of the loss of triangulation. The objective of this study is to compare classic transumbilical LESS nephrectomy with needlescopic-assisted laparoscopy (NAL) surgery. In doing so, we evaluated whether the addition of a single 2-mm subcostal port could restore triangulation while not jeopardizing recovery or cosmetic outcome in the porcine model. MATERIALS AND METHODS Ten female farm pigs were randomized to laparoscopic nephrectomy with either LESS or NAL. In LESS, a TriPort was placed through a single 2.5-cm umbilical incision. In NAL, 5- and 10-mm ports were placed in the umbilicus and a 2-mm port was placed in the midclavicular line. Preoperative, perioperative, and postoperative parameters were compared. Variables were analyzed with the Wilcoxon signed-rank test and two-tailed Fisher exact test. Cosmesis was evaluated objectively using the Vancouver Scar Scale and subjectively by a blinded dermatologist. A cost analysis was performed. RESULTS Estimated blood loss was minimal in both groups (28.8 mL in LESS and 9.4 mL in NAL). Operative time was significantly shorter in NAL (103 vs 150 min; P<0.001). There was no difference in complications (2 vs 1; P=0.500), objective cosmesis (3.9 vs 3.8; P>0.2), or subjective cosmesis (2 vs 3; P=0.500). The NAL protocol had significantly lower disposable equipment costs ($363 vs $1696). CONCLUSIONS The addition of a 2-mm subcostal port and the restoration of triangulation in the NAL protocol enable shorter operative times, increased surgeon comfort, improved technical ease, and lower costs while maintaining the scarless cosmesis of the traditional LESS protocol.
Laparoendoscopic single-site extraperitoneal inguinal hernia repair: initial experience in 10 patients.

BACKGROUND AND PURPOSE Recent technical advances and a trend toward laparoscopic single incision surgery have led us to explore the feasibility of laparoendoscopic single-site (LESS) hernia repair. PATIENTS AND METHODS We present our technique and initial experience with LESS extraperitoneal inguinal hernia repair in 10 consecutive men with unilateral inguinal hernias. Age range was 43.7 (28-64) years. Mean body mass index was 28 (range 24-30). Six were left inguinal hernias. There were six indirect and four direct hernias. Three patients had undergone previous open appendectomy. Incarcerated or bilateral hernias were excluded from our initial series. All cases were performed by three surgeons who were experienced in conventional totally extraperitoneal laparoscopic hernia repair as well as experienced in LESS. A literature review of current single-port inguinal hernia repair data is also presented. RESULTS The mean operative time was 53 minutes (range 45-65 min). The average length of skin incision was 2.8 cm (range 2.3-3.2 cm). No drain was necessary in any of the patients, while no recordable bleeding was observed. There were no intraoperative or immediate postoperative complications. Hospitalization period was 2 days for all patients. After a limited follow-up of 1 month, there have been no recurrences and no complaints of testicular pain. The results of the current series compare favorably with those found in a literature review. CONCLUSION LESS extraperitoneal inguinal hernia repair is both feasible and safe, although more technically demanding than its conventional laparoscopic counterpart. Although the cosmetic result with the former approach may prove superior, there are standing questions regarding the complications and long-term outcome. Randomized and if possible blinded trials that compare conventional and single-incision laparoscopic hernia repair may help to distinguish the most advantageous technique.
New Early Cretaceous palaeomagnetic pole from Córdoba Province (Argentina): revision of previous studies and implications for the South American database

SUMMARY A continental sequence of red beds and interbedded basaltic layers crops out in the Sierra Chica of Cordoba Province, Argentina (31.5°S, 64.4°W). This succession was deposited in a half-graben basin during the Early Cretaceous. We have carried out a palaeomagnetic survey on outcrops of this basin (147 sites in seven localities). From an analysis of IRM acquisition curves and detailed demagnetization behaviour, three diVerent magnetic components are identified in the volcanic rocks: components A, B and X are carried by single- or pseudo-single-domain (titano) magnetite, haematite and multidomain magnetite, respectively. Component A is interpreted as a primary compo- nent of magnetization because it passes conglomerate, contact, tilt and reversal tests. The carrier of the primary magnetization, fine-grained (titano)magnetite, is present in basalts with a high degree of deuteric oxidation. This kind of oxidation is interpreted to have occurred during cooling. Components B and X are discarded because they are interpreted as recent magnetizations. In the sedimentary rocks, haematite and magnetite are identified as the carriers of remanence. Both minerals carry the same component, which passes a reversal test. The calculated palaeomagnetic pole, based on 55 sites, is Lat. 86.0°S, Long. 75.9° E( A 95 =3.3, K=35). This palaeomagnetic pole supersedes four with anomalous positions reported in previous papers.
Effect of storage temperatures and stresses on the survival of Salmonella spp. in halva

The presence of Salmonella spp. in halva has been associated with foodborne illnesses and product recalls from the markets. This study investigated the effect of environmental stresses on the survival of Salmonella spp. in halva during storage for 12 months at 10 and 25°C (log (N0/N) g−1). Halva samples were inoculated with a cocktail of four strains of unstressed, desiccation stressed or heat stressed Salmonella (106–107 CFU per gram). In general, survival of Salmonella spp. in halva decreased significantly (P ˂ 0·05) as storage time and temperature increased. At the end of halva shelf life at 10°C, the initial populations of unstressed, desiccation stressed or heat stressed Salmonella spp. decreased by 2·7, 2·6 or 2·8 log CFU per gram (reduction rate c. 0·2 log CFU per month), respectively. While at 25°C, the populations decreased 5·2, 6·7 or 6·3 log CFU per gram, respectively (reduction rate c. 0·4–0·5 log CFU per month). The populations of stressed Salmonella spp. in halva samples were not significantly different (P ≥ 0·05) from populations of unstressed cells during storage at 10 and 25°C, except during the last 3 months of storage at 25°C when populations of unstressed cells were higher (P < 0·05). Exposing Salmonella spp. to desiccation or heat stress prior product contamination may play a role in Salmonella spp. survival in halva during storage.
Amamentação exclusiva de recém-nascidos prematuros: percepções e experiências de lactantes usuárias de um serviço público especializado

OBJETIVO: Investigar percepcoes e vivencias das maes de recem-nascidos prematuros que amamentaram exclusivamente do 4o ao 6o mes de vida. METODOS: Estudo seccional exploratorio, fundamentado no metodo qualitativo. Utilizaram-se entrevistas nao-diretivas, individuais, junto a oito mulheres, maes de prematuros atendidas no ambulatorio de follow-up da Maternidade Escola Assis Chateaubriand, servico vinculado ao Sistema Unico de Saude. A analise tematica das falas apontou um eixo em torno do qual foram agrupados quatro nucleos de sentido: os sentimentos das maes ao vivenciarem o contato inicial com os recem-nascidos prematuros; o apoio dos profissionais as maes de prematuros; a decisao das maes de prematuros em amamentar exclusivamente e a convivencia com o metodo mae-canguru. RESULTADOS: A analise revelou que cada mae vivencia o aleitamento materno exclusivo de maneira singular. A decisao de amamentar o prematuro esta relacionada ao reconhecimento da importância do leite materno para a saude do filho. Contudo, o suporte fornecido pela Instituicao, a partir do apoio dos profissionais as maes de prematuros, tal como se observa no servico analisado, revela-se como elemento decisivo para a pratica exclusiva do aleitamento materno. CONCLUSAO: Amamentar exclusivamente os prematuros ainda e um desafio para algumas maes, mas e possivel, desde que haja determinacao, suporte apropriado da familia, da rede social e, em especial, dos profissionais de saude.
Novel screening strategy reveals a potent Bacillus antagonist capable of mitigating wheat take‐all disease caused by Gaeumannomyces graminis var. tritici

Take‐all is a severe root disease of wheat worldwide that is caused by the soilborne fungal pathogen Gaeumannomyces graminis var. tritici (Ggt). In this study, 272 Bacillus isolates were screened for their antifungal activity in vitro to Ggt. Of the 128 strains that demonstrated an antagonistic action, 24 of these exhibited at least three of the four plant growth promotion parameters (i.e. indole acetic acid and siderophore production, inorganic phosphorus solubilization and organic phosphorus solubilization) that were tested in wheat plants. The most effective strain found was Bacillus subtilis Pnf‐12; its disease reduction effect reached 69%. Pnf‐12 also caused a significant improvement (P < 0·05) in the root and shoot weights of wheat plants, though their root length and shoot height were similar to the noninoculated treatment (P > 0·05). The mechanism for this disease control may be linked to the production of the antifungal lipopeptides surfactin, iturin and fengycin production, all of which were detected in the cell‐free supernatant of Pnf‐12.
Sysmex UF‐1000i flow cytometer to screen urinary tract infections: the URISCAM multicentre study

The new Sysmex UF‐1000i analyzer – which incorporates bacteria morphology distinction – allows to automatically screen samples to be cultured at microbiology laboratories. We have evaluated the feasibility and accuracy of Sysmex UF‐1000i to screen urinary tract infections (UTIs). A total amount of 2468 urine samples from six Spanish hospitals were analysed. Demographic and clinical data such as age, gender, source and sample type, preserving conditions, cytometer parameters (bacteria, leucocytes and bacteria morphology) as well as urine culture results (gold standard) were recorded. After applying data mining techniques, the variables of age, bacteria count and rod morphology were defined as predictive variables of UTIs. By using the UF‐1000i in combination with a predictive algorithm of three decision rules, we could identify 94·9 and 47·4% positive and negative urine samples, respectively, with a negative predictive value of 97 and only 1·17% diagnostic error. This error was reduced down to 0·4% when contaminated samples were excluded. Our results show that flow cytometry parameters together with age, by means of a predictive algorithm model, can be used to screen UTIs. Its implementation would avoid culturing 38% of urine samples, and therefore, would reduce time to diagnosis with a discrete false negative ratio.
Comparison of clinical examination and ultrasonography in the diagnosis of acute appendicitis

This study was undertaken to compare clinical examination and ultrasonography (USG) in the diagnosis of acute appendicitis and to establish their accuracy in the diagnosis of acute appendicitis. 100 patients who presented to the emergency department with a clinical diagnosis of acute appendicitis were subjected to USG. After USG a specific diagnosis was made. Patients underwent appendicectomy on the basis of the surgeon‘s final clinical impression after correlating with USG findings. Histopathological examination of the appendicectomy specimen was taken as the gold standard for the diagnosis of acute appendicitis. Appendicectomy was performed in 74 patients. Out of these 74 cases, only 66 had appendicitis on histopathological examination. Eight normal appendixes were removed. Twenty-six patients were prevented from surgery after USG had shown an alternative diagnosis for the cause of pain in right iliac fossa. Clinical examination thus had a sensitivity and Positive Predictive Value (PPV) of 66%. USG examination made a preoperative diagnosis of acute appendicitis in 62 of the 66 patients. However the remaining 4 cases with appendicitis were missed by USG. USG had a sensitivity of 93.93%, specificity of 100%, PPV of 100%, NPV of 89.47% and an overall accuracy of 96% in the diagnosis of acute appendicitis. USG is thus a sensitive and specific imaging modality in the diagnostic work up of patients with right iliac fossa pain. USG may improve the diagnostic accuracy in patients with suspected acute appendicitis. Journal of College of Medical Sciences-Nepal, 2011, Vol-7, No-2, 34-40 DOI: http://dx.doi. org/10.3126/jcmsn.v7i2. 6678
Aneurysmal bone cyst: The role of cryosurgery as local adjuvant treatment

Aneurysmal bone cysts (ABCs) are most often treated with intralesional surgery (curettage) and additional bone grafting. There is debate on whether or not to use adjuvant therapy to decrease the local recurrence rate. This study is done to assess the outcome of curettage and cryosurgery as a treatment of ABC.
Involvement of ERK, p38 and NF‐κB signal transduction in regulation of TLR2, TLR4 and TLR9 gene expression induced by lipopolysaccharide in mouse dendritic cells

Toll‐like receptors (TLR) are sentinel receptors capable of recognizing pathogen‐associated molecule patterns (PAMP) such as lipopolysaccharide (LPS) and CpG‐containing oligonucleotides (CpG ODN). TLR2 and TLR4 are major receptors for Gram‐positive and Gram‐negative bacterial cell wall components, respectively. TLR9 is necessary for CpG signalling. LPS or CpG ODN can activate immature dendritic cells (DC) and induce DC maturation characterized by production of cytokines, up‐regulation of co‐stimulatory molecules, and increased ability to activate T cells. However, little is known regarding the regulation of TLR gene expression in mouse DC. In this study, we investigated the regulation of TLR2, TLR4 and TLR9 gene expression by LPS in murine immature DC. TLR2, TLR4 and TLR9 mRNA were up‐regulated following LPS stimulation. The up‐regulation of TLR9 expression coincided with significantly increased production of tumour necrosis factor‐α induced by LPS plus CpG ODN. While inhibition of extracellular signal‐related kinase and NF‐κB activation suppressed the up‐regulation of the expression of TLR2, TLR4 and TLR9 mRNA, inhibition of p38 kinase prevented the up‐regulation of TLR2 and TLR4 mRNA expression but enhanced the up‐regulation of TLR9 expression. These results demonstrated that TLR2, TLR4 and TLR9 gene expression was differently regulated by LPS in mouse immature DC. Up‐regulation of TLR2, TLR4 and TLR9 expression by LPS might promote the overall responses of DC to bacteria and help to explain the synergy between LPS and other bacterial products in the induction of cytokine production.
‘Where were your clothes?’ Eliciting descriptions of clothing placement from children alleging sexual abuse in criminal trials and forensic interviews

PURPOSE The present study examined how children alleging sexual abuse are asked about clothing placement during abusive episodes, both in criminal trials and forensic interviews. The placement of clothing is of great importance, because it facilitates distinguishing abusive touch from non-abusive touch, as well as the severity of abuse when the touching is in fact sexual. If clothing has not been removed, then sexual abuse appears less likely and certain types of sexual contact are physically impossible (or at least highly improbable). METHODS We examined how trial attorneys (n = 142) and forensic interviewers in investigative interviews (n = 155) questioned 5- 12-year-olds about the location of clothing during alleged sexual abuse. To do so, we identified all question-answer pairs that included references to clothing placement, and coded for the clothing item mentioned, whether the interviewer elicited information about clothing placement or the child spontaneously provided such information, question-type, and response-type. RESULTS Discussions about clothing placement were commonplace in both settings, particularly in court. Fewer than one in five question-answer pairs about clothing placement were spontaneous mentions by children; the questioner elicited most discussions. When interviewers asked wh- questions rather than yes/no and forced-choice questions, children provided more elaboration, more detailed clothing information, and were over six times more likely to describe clothing placement in a fashion that could not be captured by a single preposition (e.g., neither on nor off). CONCLUSIONS The findings suggest that descriptions of clothing placement are subject to serious misinterpretation when closed-ended questions are asked.
Bacteroides paurosaccharolyticus sp. nov., isolated from a methanogenic reactor treating waste from cattle farms.

A strictly anaerobic bacterial strain (WK042(T)) was isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms in Japan. Cells were Gram-staining-negative, non-motile, non-spore-forming rods. Growth was stimulated well by haemin, and was enhanced by cobalamin (vitamin B(12)). Strain WK042(T) utilized arabinose, xylose, glucose, mannose and aesculin as preferred substrates. Maltose, dextrin, glycogen, starch and pectin were also utilized, although growth on these substrates was much slower. The strain produced acetate, propionate and succinate from these saccharides. The strain was slightly alkaliphilic, with optimum growth at pH 7.7. The temperature range for growth was 10-40 °C, the optimum being 35 °C. The strain was sensitive to bile. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(17 : 0) 3-OH and C(15 : 0). Menaquinone 11 (MK-11) was the major respiratory quinone and the genomic DNA G+C content was 41.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed the strain in the phylum Bacteroidetes. Strain WK042(T) was related distantly to the type strains of species in the cluster including Bacteroides massiliensis, Bacteroides vulgatus and Bacteroides dorei (91-92 % 16S rRNA gene sequence similarity). Based on data from the present phylogenetic, physiological and chemotaxonomic analyses, strain WK042(T) is considered to represent a novel species of the genus Bacteroides, for which the name Bacteroides paurosaccharolyticus sp. nov. is proposed. The type strain is WK042(T) (=JCM 15092(T) =DSM 21004(T)).
Potential role of soluble CD40 in the humoral immune response impairment of uraemic patients

CD40/CD154 interaction is essential for both humoral and cellular immune response. We investigated whether this interaction could be altered in patients with kidney failure who are known to present an impaired immune response. To that aim, we measured the levels of the soluble form of CD40 (sCD40), which is known to interfere with CD40/CD154 interaction, in 43 chronic renal failure patients, 162 hemodialysed patients, and 83 healthy donors. Uraemic and haemodialysed patients presented a three‐ and fivefold increase, respectively, of the antagonist soluble form of CD40 in their serum, when compared to healthy subjects. Serum sCD40 levels correlated with those of creatinine in uraemic non‐haemodialysed patients. While sCD40 is widely excreted in urine of healthy individuals, it is not eliminated by dialysis sessions on classic membranes. The return to a normal kidney function in nine haemodialysed patients who received renal transplantation, leads to a rapid decrease of serum sCD40 levels. This natural sCD40 exhibited multimeric forms and was able to inhibit immunoglobulin production by CD154‐activated B lymphocytes in vitro. Furthermore, the positive correlation we observed between the serum levels of sCD40 and the deficient response to hepatitis B vaccination in uraemic patients suggests that sCD40 also compromises the humoral response in vivo.
Urolithiasis location and size and the association with microhematuria and stone-related symptoms.

PURPOSE To conduct a study to assess the association between calculus location and size and the incidence of both microhematuria and symptoms of urolithiasis in a urology office environment. PATIENTS AND METHODS After Institutional Review Board approval, a prospective study was conducted with data from 100 consecutive patients who presented to our office with documented urolithiasis. The location (caliceal, pelvic, or ureteral) and size (<or ≥ 8 mm) of each calculus was determined from available diagnostic radiographs. The incidence of microhematuria was ascertained via a urine dipstick and microscopic examination. The presence of any symptoms associated with urolithiasis, including pain, subjective fever or chills, or urinary urgency, was recorded. RESULTS A total of 111 stones were found in the study population resulting in a 45.9% incidence of microhematuria. In patients with renal pelvic and ureteral stones, 67.6% demonstrated microhematuria vs 36.4% with caliceal stones, P=0.0035. For stones ≥ 8 mm, 62.5% were positive for microhematuria vs 29.1% of stones <8 mm, P=0.0006. Ureteral or renal pelvic stones caused the most symptoms (70.6%) compared with caliceal stones (16.9%), P=0.0001. In those patients who reported pain associated with urolithiasis, 65.6% had concomitant microhematuria vs 36.8% in those without pain, P=0.0097. CONCLUSIONS Urinary calculus location and size are associated with the incidence of microhematuria and stone-related symptoms. Pain related to urolithiasis may be a positive predictor for the presence of microhematuria.
Kinetics and prediction of HBsAg loss during therapy with analogues in patients affected by chronic hepatitis B HBeAg negative and genotype D

In patients affected by chronic hepatitis because of HBV infection, long‐term suppressive therapy with nucleos(t)ides analogues in the HBeAg− patients has shown low effects on HBsAg titre (qHBsAg) decrease, and HBsAg loss is difficult to achieve. Thus, in this type of patients the main goals of antiviral therapy is the suppression of HBV‐DNA and ALT normalization.
Liver disease in adult transfusion‐dependent beta‐thalassaemic patients: investigating the role of iron overload and chronic HCV infection

Iron overload and hepatitis‐C virus (HCV) infection, have been implicated in the evolution of liver disease, in patients with transfusion‐dependent beta‐thalassaemia major (BTM). However, the impact of these factors in late stages of liver disease in adults with BTM, has not been extensively studied.