Miracle-dz/UniFAR-FTUs huggingface dataset:
The assumed assimilation of cholesterol by Lactobacilli and Bifidobacterium bifidum is due to their bile salt-deconjugating activity

To study the mechanism of the propsed assimilation of cholesterol, we cultured various strains of Lactobacillus acidophilus and a Bifidobacterium sp. in the presence of cholesterol and oxgall. During culturing, both cholesterol and bile salts were precipitated. Because of bacterial bile salt deconjugation, no conjugated bile salts were observed in either the culture fluids or the pellets. During incubation, the cell count and optical density decreased. The degree of precipitation of bile salts and of cholesterol was dependent on the culture conditions. If L. acidophilus RP32 was cultured under acidifying conditions, the degree of precipitation of deconjugated bile salts was higher than if the pH was maintained at 6.0. Under acidifying conditions, cholesterol was coprecipitated with the bile salts, whereas in pH-controlled cultures, no coprecipitation of cholesterol was observed. From control experiments with different mixtures of bile salts, it appeared that coprecipitation of cholesterol during culturing was a result of formation of deconjugated bile salts, which have a decreased solubility at pH values lower than 6.0. It is concluded that the removal of cholesterol from the culture medium by L. acidophilus RP32 and other species is not due to bacterial uptake of cholesterol, but results from bacterial bile salt-deconjugating activity.
The prevalence of neutralizing antibodies against AAV serotype 1 in healthy subjects in China: Implications for gene therapy and vaccines using AAV1 vector

Recombinant adeno‐associated virus serotype 1 (AAV1) has attracted tremendous interest as a promising vector for gene therapy and vaccine applications. However, the presence of AAV1 neutralizing antibodies as a consequence of exposure to wild type AAV1 can limit significantly effective gene transfer for biologics based AAV1 vector. Prior studies have reported that a prevalence of AAV1 neutralizing antibodies ranged from 10% to 50% in different countries around the world, and up to 79% in Dutch subjects. However, few studies have reported on the AAV1 neutralizing antibody prevalence in Chinese subjects. In this study, a high‐throughput luciferase‐based virus neutralization assay was established and standardized for critical parameters, including the appropriate cell line, and the optimal viral infection dose, and the infection time with homologous AAV1 vaccinated mice and guinea pig sera. Then, a total of 500 healthy individual serum samples from two separate regions of China were screened for the AAV1 neutralizing antibodies by conducting a non‐randomized, cross‐sectional analysis. Interestingly, a high prevalence of AAV1 neutralizing antibody (69.8%) was found in all individuals. There was significant difference observed for prevalence by gender (P = 0.042), age range (P = 0.011) and geographic origin (P < 0.001). The percentage of positive AAV1 neutralizing antibodies (NT50 > 10) in teenagers (year <18, as of 2012) was significant lower than that of adults (19–56, as of 2012) (P = 0.011), indicating the optimal vaccination period of childhood. The current study provides a useful insight for the future development of AAV1‐based vaccination and gene therapy strategies in Beijing and Anhui provinces of China. J. Med. Virol. 85:1550–1556, 2013. © 2013 Wiley Periodicals, Inc.
Postnatal growth retardation: a universal problem in preterm infants

Background: Previous data from this unit suggest that postnatal growth retardation (PGR) is inevitable in preterm infants. However, the study was performed in a single level III neonatal intensive care unit and applicability of the findings to other level III or level I–II special care baby units was uncertain. Objectives: To examine postnatal hospital growth and to compare growth outcome in preterm infants discharged from four level III tertiary care units and 10 level I–II special care baby units in the former Northern Region of the United Kingdom. Subjects/methods: Preterm infants (⩽ 32 weeks gestation; ⩽ 1500 g) surviving to discharge were studied. Infants were weighed at birth and discharge. Body weight was converted into a z score using the British Foundation Growth Standards. To ascertain the degree of PGR, the z score at birth was subtracted from the z score at discharge. Data were evaluated using a combination of split plot (level III v I–II = main factor; individual centre = subfactor) and stepwise regression analyses. Results were considered significant at p < 0.05. Results: A total of 659 (level III, n = 335; level I–II, n = 324) infants were admitted over a 24 month period (January 1998–December 1999). No differences were detected in birth characteristics, CRIB score (a measure of illness in the first 24 hours of life), length of hospital stay, weight gain, weight at discharge, or degree of PGR between infants discharged from level III and level I–II units. Significant variation was noted in length of hospital stay (∼35%; p < 0.001), weight gain (∼33%; p < 0.001), weight at discharge (∼20%; p < 0.001), and degree of PGR (∼200%; p < 0.001) between the level III units. Even greater variability was noted in the duration of hospital stay (∼40%; p < 0.001), weight gain (∼60%; p < 0.001), weight at discharge (∼40%, p < 0.001), and degree of PGR (∼300%, p < 0.001) between the level I–II units. Conclusions: These data stress the variable but universal nature of PGR in preterm infants discharged from level III and I–II neonatal intensive care units and raise important questions about nutritional support of these infants before and after hospital discharge.
Mucosal Defense against Gastrointestinal Nematodes: Responses of Mucosal Mast Cells and Mouse Mast Cell Protease 1 during PrimaryStrongyloides venezuelensis Infection in FcRγ-Knockout Mice

ABSTRACT A possible role for the γ subunit of immunoglobulin Fc receptors (FcR) in mucosal defenses against intestinal nematode parasites was studied using age-matched FcRγ-knockout (FcRγ−/−) and wild-type (FcRγ+/+) C57BL/6 mice. Mice were infected subcutaneously with 3,000 infective larvae of Strongyloides venezuelensis, and the degree of infection was monitored by daily fecal egg counts and adult worm recovery on days 8 and 13 postinfection. Mucosal mast cell (MMC) responses were assayed by in situ intestinal mast cell counts in stained histological sections of the jejunum and by measuring mouse mast cell protease 1 (MMCP-1) release in serum using sandwich enzyme-linked immunosorbent assay. FcRγ−/− mice had significantly higher egg counts (P < 0.01) and numbers of adult worms (P < 0.05) than FcRγ+/+mice, but mastocytosis and serum MMCP-1 release were comparable. It was concluded that MMCP-1 release may be spontaneous, does not depend on mast cell degranulation via the FcRγ signaling system, and appears to play no role in the expulsion of S. venezuelensis. The delay in worm expulsion in the FcRγ−/− mice might be related to inability of the MMC to degranulate and release effector molecules other than MMCP-1, since FcRγ deletion abrogates mast cell degranulative responses.
Reestimating date of delivery in multifetal pregnancies.

OBJECTIVE To clarify the optimal estimated date of delivery for multifetal pregnancies. DESIGN, SUBJECTS, AND SETTING A retrospective study of all 88,936 infants born of multifetal pregnancies and all 6,020,542 infants born of singleton pregnancies that occurred at 26 weeks or more of gestation between 1989 and 1993 in Japan. MAIN OUTCOME MEASURE Incidence of stillbirth and early neonatal death according to gestational age at delivery. RESULTS The mean +/- SD duration of pregnancy was 37.0 +/- 2.7 weeks for multifetal pregnancies and 39.6 +/- 1.6 weeks for singleton pregnancies. In multifetal pregnancies, the incidence of stillbirth and of early neonatal death gradually declined until 37 to 38 weeks' gestation and then increased. These parameters in singleton pregnancies declined until 39 weeks' gestation before increasing. The lowest incidence of perinatal death (Stillbirth plus early neonatal death) seen at 38 weeks' gestation in multifetal pregnancies corresponded to that seen at 43 weeks' gestation in singleton pregnancies (10.5 vs 9.7 per 1000 infants). The fist of perinatal death was more than 6 times as high for fetuses of multifetal pregnancies born at 37 weeks or later than for singleton fetuses born at 40 weeks or later (relative risk, 6.6; 95% confidence internal, 6.1 - 7.1). CONCLUSION Fetuses of multifetal pregnancies are at an increased risk of death after reaching the normative gestational age for singleton pregnancies. Limiting the estimated date of delivery to 37 to 38 weeks may be appropriate in multifetal pregnancies.
Insights from multiple structures of the shell proteins from the β‐carboxysome

Carboxysomes are primitive bacterial organelles that function as a part of a carbon concentrating mechanism (CCM) under conditions where inorganic carbon is limiting. The carboxysome enhances the efficiency of cellular carbon fixation by encapsulating together carbonic anhydrase and the CO2‐fixing enzyme ribulose‐1,5‐bisphosphate carboxylase/oxygenase (RuBisCO). The carboxysome has a roughly icosahedral shape with an outer shell between 800 and 1500 Å in diameter, which is constructed from a few thousand small protein subunits. In the cyanobacterium Synechocystis sp. PCC 6803, the previous structure determination of two homologous shell protein subunits, CcmK2 and CcmK4, elucidated how the outer shell is formed by the tight packing of CcmK hexamers into a molecular layer. Here we describe the crystal structure of the hexameric shell protein CcmK1, along with structures of mutants of both CcmK1 and CcmK2 lacking their sometimes flexible C‐terminal tails. Variations in the way hexamers pack into layers are noted, while sulfate ions bound in pores through the layer provide further support for the hypothesis that the pores serve for transport of substrates and products into and out of the carboxysome. One of the new structures provides a high‐resolution (1.3 Å) framework for subsequent computational studies of molecular transport through the pores. Crystal and solution studies of the C‐terminal deletion mutants demonstrate the tendency of the terminal segments to participate in proteinprotein interactions, thereby providing a clue as to which side of the molecular layer of hexameric shell proteins is likely to face toward the carboxysome interior.
Phytochemical Compositions and Biological Activities of Essential Oil from Xanthium strumarium L.

The chemical composition of the essential oil (EO) from fresh cocklebur (Xanthium strumarium L.) leaves was investigated by GC-MS. The antimicrobial activity of the EO was tested against Gram-positive and Gram-negative bacteria and fungi. Scolicidal activity was assayed against Echinococcus granulosus protoscolices. In total, 34 compounds were identified, accounting for 98.96% of the EO. The main compounds in the EO were cis-β-guaiene (34.2%), limonene (20.3%), borneol (11.6%), bornyl acetate (4.5%), β-cubebene (3.8%), sabinene (3.6%), phytol (3.1%), β-selinene (2.8%), camphene (2.2%), α-cubebene (2.4%), β-caryophyllene (1.9%), α-pinene (1.8%) and xanthinin (1.04%). The antibacterial and antifungal screening of the EO showed that all assayed concentrations significantly inhibited the growth of Staphylococcus aureus, Bacillus subtilis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Candida albicans and Aspergillus niger (MIC = 0.5 ± 0.1, 1.3 ± 0.0, 4.8 ± 0.0, 20.5 ± 0.3, 55.2 ± 0.0 and 34.3 ± 0.0 µg/mL, respectively). The scolicidal assay indicated that the EO exhibited a significant activity against E. granulosus protoscolices. To the best of our knowledge, this is the first report on the scolicidal activity of X. strumarium. Because of the emergence of antimicrobial drug resistance, the study of new effective natural chemotherapeutic agents, such as the X. strumarium EO, possibly with low side effects, represents a very promising approach in biomedical research.
Immunization coverage among splenectomized patients: Results of an ad hoc survey in Puglia Region (South of Italy)

ABSTRACT Patients with anatomic or functional asplenia have a 10–50 times higher risk than general population to develop Overwhelming Post-Splenectomy Infection. Evidences are unanimous in recommending splenectomised patients to receive meningococcal, antipneumococcal and Haemophilus influenzae type B vaccinations according to a specific timing. In Italy there are no current data on the immunisation coverage in these patients. This study aims to investigate immunisation coverage in patients undergoing elective or urgent splenectomy for 2012–2013 in the 3 Apulian hospitals. The patients discharged with the code ICD-9-CM 41.5 - "Total splenectomy" were enrolled. The administration of vaccines was verified through consultation of medical records, archives of general practitioners and vaccination offices. In the study period, 166 subjects underwent splenectomy and none of them received vaccinations during hospitalization. 25 splenectomised patients (15.1%) received at least one of the recommended vaccinations. 21 patients (12.6%) received vaccine against Streptococcus pneumonia, 13 (7.8%) meningococcal vaccine, 10 patients (6%) Haemophilus influenzae type B vaccine. The low vaccination coverage could be due both to poor perception of the risk of infection and to a lack of knowledge on vaccinations by surgeons. For this reason it is necessary to draw up and share operational protocols that establish the administration of vaccines.
A Gene’s‐Eye View of Symbiont Transmission

Symbiotic associations between species are ubiquitous, but we only poorly understand why some symbioses evolve to be mutualistic and others to be parasitic. One prominent hypothesis holds that vertical transmission of symbionts from host parents to their offspring selects for symbionts that are benign or beneficial, while horizontal transmission of symbionts among unrelated hosts selects for symbionts that are less beneficial or outright harmful. A long‐standing challenge to this hypothesis, however, is the existence of selfish genetic elements (SGEs). SGEs are passed exclusively from parent to offspring and are able to spread and persist in populations despite reducing the fitness of their hosts. Here I show that SGEs are in fact consistent with the transmission mode hypothesis if one measures transmission from the perspective of host genes instead of host organisms. Both meiotic drive genes and cytoplasmic sex ratio distorters require horizontal transmission, in the form of outbred sex, to spread as parasites. Transmission from parent to offpsring does not constrain SGEs to evolve toward mutualism. The gene‐centered perspective I present here is applicable to symbioses at all levels of selection and brings closer together our understandings of cooperation within and between species.
County-scale biomass map comparison: a case study for Sonoma, California

ABSTRACT The amount of carbon stored in forests affects a wide range of regional- to global-scale climate change processes. However, current maps often show large differences in carbon accounting. In this study, we present a framework to evaluate and compare multiple recent biomass maps at the county scale (4119 km2). We first compare the differences in the forest and non-forest areas at the pixel and county levels from multiple maps. Map-based estimates of county-level mean and total biomass are compared to the United States Forest Service (USFS) sample-based estimates. Comparison of raster-based biomass products shows differences in mean and total biomass at both pixel- and county-levels. Despite all the maps using USFS's plot data for model training, only the three active sensor derived products compare well to USFS's estimates of total biomass (within 10%), while the three passive sensor derived map products underestimated total biomass by as much as 47%. Our evaluation demonstrates that the biomass map generated using combined Light Detection and Ranging (LiDAR) and auxiliary data achieve accurate estimates at plot-level (R2 = 0.67; RMSE = 97.9 Mg.ha-1). This comparison study confirmed that missing direct height information either from active sensors tends to underestimate total biomass and mean biomass density at county-level.
Nogo Receptor 1 Confines a Disinhibitory Microcircuit to the Critical Period in Visual Cortex

A characteristic of the developing mammalian visual system is a brief interval of plasticity, termed the “critical period,” when the circuitry of primary visual cortex is most sensitive to perturbation of visual experience. Depriving one eye of vision (monocular deprivation [MD]) during the critical period alters ocular dominance (OD) by shifting the responsiveness of neurons in visual cortex to favor the nondeprived eye. A disinhibitory microcircuit involving parvalbumin-expressing (PV) interneurons initiates this OD plasticity. The gene encoding the neuronal nogo-66-receptor 1 (ngr1/rtn4r) is required to close the critical period. Here we combined mouse genetics, electrophysiology, and circuit mapping with laser-scanning photostimulation to investigate whether disinhibition is confined to the critical period by ngr1. We demonstrate that ngr1 mutant mice retain plasticity characteristic of the critical period as adults, and that ngr1 operates within PV interneurons to restrict the loss of intracortical excitatory synaptic input following MD in adult mice, and this disinhibition induces a “lower PV network configuration” in both critical-period wild-type mice and adult ngr1−/− mice. We propose that ngr1 limits disinhibition to close the critical period for OD plasticity and that a decrease in PV expression levels reports the diminished recent cumulative activity of these interneurons. SIGNIFICANCE STATEMENT Life experience refines brain circuits throughout development during specified critical periods. Abnormal experience during these critical periods can yield enduring maladaptive changes in neural circuits that impair brain function. In the developing visual system, visual deprivation early in life can result in amblyopia (lazy-eye), a prevalent childhood disorder comprising permanent deficits in spatial vision. Here we identify that the nogo-66 receptor 1 gene restricts an early and essential step in OD plasticity to the critical period. These findings link the emerging circuit-level description of OD plasticity to the genetic regulation of the critical period. Understanding how plasticity is confined to critical periods may provide clues how to better treat amblyopia.
Prenatal growth markers in schizophrenia: a monozygotic co-twin control study.

OBJECTIVE This co-twin study investigated monozygotic twins who were discordant for schizophrenia for evidence of prenatal growth differences between the affected and well co-twins. METHOD Four dermatoglyphic markers of prenatal growth were obtained by established procedures from 26 monozygotic twin pairs discordant for schizophrenia, 13 monozygotic twin pairs concordant for schizophrenia, and several normal monozygotic twin samples. RESULTS The a-b ridge count differences between the affected and well co-twins were greater than those found for concordant and normal monozygotic pairs. In comparison with their well co-twins, the affected twins, in discordant pairs, had developed fewer epidermal ridges in the a-b interdigital area of their right palms. In contrast, no significant differences were found between the affected twins and their well co-twins on markers associated with fetal development before 13 or after 15 weeks estimated gestational age. CONCLUSIONS Because the a-b ridges are known to complete development between 13 and 15 weeks estimated gestational age, the results provide physical evidence suggesting that the schizophrenia-affected monozygotic twins alone experienced a time-specific and time-limited dysgenesis during this time. Commonalities in the ontogeny of epidermal and neurological structures are discussed.
Long-Term Highly Active Antiretroviral Therapy in Chronic HIV-1 Infection: Evidence for Reconstitution of Antiviral Immunity

In this study we investigated the long-term effect of highly active antiretroviral therapy (HAART) on HIV-specific CD4+ T-cell responses in comparison with virus-specific CD4+ T-cell responses against the persistent herpes viruses cytomegalovirus (CMV) and Epstein-Barr virus (EBV). To this end, HIV- and herpes virus-specific cellular immune responses were measured longitudinally in 10 seroconverters with long-term follow-up including 55 months of successful suppression of viral load by HAART. HIV- and CMV-specific CD4+ T cells producing interferon-γ (IFNγ) or interleukin-2 (IL-2) were analysed as well as proliferative capacity. EBV-specific CD4+ T cells were determined using a 12-day ex vivo assay. Initiation of HAART resulted in a transient increase of HIV-specific IL-2+IFNγ+CD4+ T cells and, to a lesser extent, IL-2+CD4+ T cells. Long-term HAART resulted in an increase in HIV-, CMV- and EBV-specific CD4+ T-cell proliferative capacity. The increase in HIV- and herpes-virus-specific CD4+ T-cell proliferative capacity after 55 months of HAART suggests that the improved proliferative response is not specific for HIV, but reflects a more general improvement of antiviral immune responses, which is induced by HAART.
Fascin stain as a potential marker of invasiveness in carcinomas of the urinary bladder: A retrospective study with biopsy and cytology correlation

The evaluation of invasion in urothelial carcinomas of the urinary bladder cannot be determined on cytology and can be particularly challenging in biopsy cases with limited sampling. Recent studies of bladder resection specimens suggest that fascin overexpression may be a marker of aggressive urothelial carcinomas and can help facilitate the assessment of invasion. In this study, we evaluated urine cytology and corresponding biopsy specimens with proven invasive urothelial carcinoma for fascin expression by immunohistochemistry. Thirty‐five patients diagnosed with positive urine cytology and biopsy‐proven invasive urothelial carcinoma between January 2003 and February 2009 were identified. We found increased fascin expression in 100% (35/35) of SurePathTM&! trade; urine cytology preparations as well as 100% (35/35) of corresponding biopsy cases with invasive urothelial carcinoma. On urine cytology, cytoplasmic fascin staining was moderate to intense in malignant tumor cell clusters and single cells and not observed in benign urothelial cells. Staining in biopsy cases was generally intense and cytoplasmic and present in both the invasive (100%) and noninvasive (31%) components of the lesion. These findings uphold the association of increased fascin expression in invasive urothelial carcinomas of the urinary bladder. We furthermore demonstrate that fascin staining can be performed successfully on SurePathTM&! trade; urine cytology preparations in which increased fascin expression correlates with invasion on biopsy. While not a definitive marker of invasion, as it is observed in in situ carcinoma, we conclude that the utilization of fascin immunohistochemistry on urine cytology might serve as a useful adjunct in predicting invasiveness in subsequent biopsies. Diagn. Cytopathol. 2010. © 2010 Wiley‐Liss, Inc.