Miracle-dz/UniFAR-FTUs huggingface dataset:
Reduction in faecal excretion of Salmonella typhimurium strain F98 in chickens vaccinated with live and killed S. typhimurium organisms

SUMMARY Chickens given orally at 4 days of age a smooth spectinomycin resistant mutant (Spcr) of Salmonella typhimurium strain F98 excreted the organism in their faeces for approximately 4 weeks. Following oral administration of a nalidixic acid resistant (Nalr) mutant of the same strain 4 weeks later when later when the chickens had virtually cleared themselves of the first infection, these chickens excreted far fewer salmonella organisms and for a shorter time than did a previously uninfected control group of chickens which were infected at the same time with the Nalr mutant. Chickens inoculated intramuscularly at 4 days developed a similar immunity to challenge and also excreted the immunizing strain in their faeces. In contrast intramuscular inoculation or incorporation into the food of formalin-killed S. typhimurium organisms had little lasting effect on the faecal excretion of the challenge strain. Two attenuated mutants of strain F98 Nalr were produced: one was a rough strain produced by lytic bacteriophage and the other was an aro A auxotrophic mutant which had been cured of the 85 kilobase–pair virulence–associated plasmid. These mutants were avirulent for chickens, mice, calves and man and when ingested by human volunteers did not persist in the faeces. When inoculated intramuscularly into chickens they produced an early reduction in faecal excretion of the challenge strain (Spcr) which was not maintained. Oral administration of both strains produced reductions in faecal excretion of the challenge strain. This was much more noticeable with the rough strain which was itself excreted for a much longer period than the parent strain.
Serum DNA methylation for monitoring response to neoadjuvant chemotherapy in breast cancer patients

Patients with large or nonoperable breast cancers often receive neoadjuvant chemotherapy to facilitate full resection of the tumor and enable conservation of the breast. However, currently available methods for evaluation of response during therapy are limited and the actual effect of the treatment is only recognized at surgery upon completion of chemotherapy. Timely assessment of response could allow individual tailoring of the treatment and save noneffective drugs and unnecessary toxicity. Here, we suggest that tumor derived DNA methylation in the serum may reflect changes in tumor burden and allow early recognition of responders versus nonresponders. In this pilot study, we collected 7 consecutive serum samples from 52 patients with locally advanced breast cancer during neoadjuvant chemotherapy. We selected RASSF1, which was methylated in more than 80% of the tumors, for serum analysis. Using the “methylation sensitive PCR and high resolution melting,” we detected RASSF1 methylation in the serum of 21 patients prior to therapy. In four patients who achieved complete pathological response, RASSF1 methylation in the serum became undetectable early during therapy. In contrast, in 17 patients that had partial or minimal pathological response, serum RASSF1 methylation persisted longer or throughout the treatment (complete versus partial response p = 0.02). These findings support further development of this assay for monitoring response during neoadjuvant therapy.
When global rule reversal meets local task switching: The neural mechanisms of coordinated behavioral adaptation to instructed multi‐level demand changes

Cognitive flexibility is essential to cope with changing task demands and often it is necessary to adapt to combined changes in a coordinated manner. The present fMRI study examined how the brain implements such multi‐level adaptation processes. Specifically, on a “local,” hierarchically lower level, switching between two tasks was required across trials while the rules of each task remained unchanged for blocks of trials. On a “global” level regarding blocks of twelve trials, the task rules could reverse or remain the same. The current task was cued at the start of each trial while the current task rules were instructed before the start of a new block. We found that partly overlapping and partly segregated neural networks play different roles when coping with the combination of global rule reversal and local task switching. The fronto‐parietal control network (FPN) supported the encoding of reversed rules at the time of explicit rule instruction. The same regions subsequently supported local task switching processes during actual implementation trials, irrespective of rule reversal condition. By contrast, a cortico‐striatal network (CSN) including supplementary motor area and putamen was increasingly engaged across implementation trials and more so for rule reversal than for nonreversal blocks, irrespective of task switching condition. Together, these findings suggest that the brain accomplishes the coordinated adaptation to multi‐level demand changes by distributing processing resources either across time (FPN for reversed rule encoding and later for task switching) or across regions (CSN for reversed rule implementation and FPN for concurrent task switching).
Pre‐ and post‐season heart rate variability in adolescent cross‐country skiers

To investigate the effects on cardiac autonomic control after a competitive cross‐country skiing season, 9 females and 8 males, 16–19 years old, performed tilt‐table heart rate variability (HRV) recordings and incremental treadmill tests before (August), and after (April the following year) the most intensive period of training and competition. Spectral analysis of HRV showed increased total variability at rest and reduced low frequency variability in the tilted position (LFtilt) at the second test (P<0.05). The female subgroup showed consistently higher high frequency (HF) and total heart rate variability than males. Total run time (RunT) increased from 18.5±1.9 min to 19.4±1.7 min (mean±SD) in the entire group (P<0.05), while VO2max only showed a non‐significant increase (0.05
Genetic patterning of embryonic inner ear development.

The commitment of the otocyst to form balance (pars superior) and hearing (pars inferior) receptors is under the control of patterning genes. Intersecting patterns of gene expression has been proposed to explain the regionalization of inner ear sensory receptor development. Insights into the roles of patterning genes is being acquired from the analysis of inner ear development of null mutation mice. An example of the consequences of the loss of expression of a single patterning gene is the effect of a null mutation of paired-box gene 2 (Pax2) on formation of the cochlea. Pax2 transcripts are expressed in the pars inferior of the otocyst and null mutant inner ears show agenesis of the cochlea. This is an example of the profound effect that loss of a single patterning gene can have on inner ear development. However, more typically there is redundancy of gene action during inner ear development as exemplified by the overlapping pattern of expression of two closely related homeobox-containing genes (i.e. Hmx2 and Hmx3) in the pars superior of the otocyst. Hmx2 and Hmx3 genes are both expressed early in otic development with Hmx3 transcripts present in the placode. However, null mutation of the Hmx3 patterning gene produced only a limited vestibular defect, and did not result in the agenesis of the vestibule. This result suggests that there is redundancy in genes that have similar patterns of regional expression in the otic anlagen.
Ethnic differences in the development of albuminuria: the DISTANCE study.

OBJECTIVES To determine whether ethnic differences in the incidence of albuminuria are present in patients with diabetes, and to identify social, behavioral, and provider factors that explain ethnic differences. STUDY DESIGN Survey follow-up design with a race-stratified baseline survey (2005-2006) in diabetic patients from a nonprofit, fully integrated healthcare system in Northern California. We followed the 10,596 respondents (30% whites, 20% blacks, 23% Hispanics, 14% Asians, and 13% Filipinos) without evidence of prevalent albuminuria at baseline. METHODS Incident albuminuria was defined by positive dipstick urinalysis (>1) or urine albumin to creatinine level (>30 mg/g), and confirmed with repeat testing at least 3 months later. RESULTS The 27,292 person-years of observation yielded 981 incident albuminuria events. Agestandardized rates of albuminuria (per 1000 person-years) ranged from 13.6 (95% confidence interval [CI] 10.5-17.0) in whites to 27.8 (CI 18.2- 38.3) in blacks. In fully adjusted Cox models, the hazard ratio for blacks (1.22, 95% CI 1.09-1.38), Asians (1.35, 95% CI 1.13-1.61), and Filipinos (1.93, 95% CI 1.61-2.32), but not Hispanics, was significantly greater than it was for whites. In some cases, point estimates changed markedly from the base model when fully adjusted for potential confounders. Moreover, adjustment for an array of potentially mediating factors explained only a small proportion of the observed ethnic disparities. CONCLUSIONS Despite uniform medical care coverage, Filipinos, blacks, and Asians with diabetes developed albuminuria at higher rates than white and Hispanic adults.
Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Activase Deficiency Delays Senescence of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase but Progressively Impairs Its Catalysis during Tobacco Leaf Development

Transgenic tobacco (Nicotiana tabacum L. cv W38) plants with an antisense gene directed against the mRNA of ribulose-1,5-biphosphate carboxylase/oxygenase (Rubisco) activase grew more slowly than wild-type plants in a CO2-enriched atmosphere, but eventually attained the same height and number of leaves. Compared with the wild type, the anti-activase plants had reduced CO2 assimilation rates, normal contents of chlorophyll and soluble leaf protein, and much higher Rubisco contents, particularly in older leaves. Activase deficiency greatly delayed the usual developmental decline in Rubisco content seen in wild-type leaves. This effect was much less obvious in another transgenic tobacco with an antisense gene directed against chloroplast-located glyceraldehyde-3-phosphate dehydrogenase, which also had reduced photosynthetic rates and delayed development. Although Rubisco carbamylation was reduced in the anti-activase plants, the reduction was not sufficient to explain the reduced photosynthetic rate of older anti-activase leaves. Instead, up to a 10-fold reduction in the catalytic turnover rate of carbamylated Rubisco in vivo appeared to be the main cause. Slower catalytic turnover by carbamylated Rubisco was particularly obvious in high-CO2-grown leaves but was also detectable in air-grown leaves. Rubisco activity measured immediately after rapid extraction of anti-activase leaves was not much less than that predicted from its degree of carbamylation, ruling out slow release of an inhibitor from carbamylated sites as a major cause of the phenomenon. Nor could substrate scarcity or product inhibition account for the impairment. We conclude that activase must have a role in vivo, direct or indirect, in promoting the activity of carbamylated Rubisco in addition to its role in promoting carbamylation.
Transsynaptic inhibition of spinal transmission by A2 botulinum toxin

Botulinum toxin A (BoNT/A) blocks synaptic transmission via the cleavage of SNAP‐25. Axonal transport of BoNT/A (A1 type botulinum toxin (A1LL) and A2 type botulinum toxin (A2NTX)) from periphery to the CNS has been described in trigeminal nerve and foreleg muscles. A1LL and A2NTX were injected into the ipsilateral soleus, and their effects on ipsilateral and contralateral contractions were compared as a measure of local and systemic/transport‐mediated effects. Spinal transmission was also measured to determine axonal and transsynaptic transport of neurotoxin. A2NTX induced faster and stronger muscle relaxation than A1LL. A1LL arrived at the contralateral muscle by almost equal transport via neural pathways and by the circulation. A2NTX was mainly transported to contralateral muscles via the blood. A1LL and A2NTX were carried from peripheral to CNS and vice versa by dual antero‐ and retrograde axonal transport through either motor or sensory neurons. Our results may point to greater potential safety in A2NTX form.
Dual Inhibition of Activin/Nodal/TGF-β and BMP Signaling Pathways by SB431542 and Dorsomorphin Induces Neuronal Differentiation of Human Adipose Derived Stem Cells

Damage to the nervous system can cause devastating diseases or musculoskeletal dysfunctions and transplantation of progenitor stem cells can be an excellent treatment option in this regard. Preclinical studies demonstrate that untreated stem cells, unlike stem cells activated to differentiate into neuronal lineage, do not survive in the neuronal tissues. Conventional methods of inducing neuronal differentiation of stem cells are complex and expensive. We therefore sought to determine if a simple, one-step, and cost effective method, previously reported to induce neuronal differentiation of embryonic stem cells and induced-pluripotent stem cells, can be applied to adult stem cells. Indeed, dual inhibition of activin/nodal/TGF-β and BMP pathways using SB431542 and dorsomorphin, respectively, induced neuronal differentiation of human adipose derived stem cells (hADSCs) as evidenced by formation of neurite extensions, protein expression of neuron-specific gamma enolase, and mRNA expression of neuron-specific transcription factors Sox1 and Pax6 and matured neuronal marker NF200. This process correlated with enhanced phosphorylation of p38, Erk1/2, PI3K, and Akt1/3. Additionally, in vitro subcutaneous implants of SB431542 and dorsomorphin treated hADSCs displayed significantly higher expression of active-axonal-growth-specific marker GAP43. Our data offers novel insights into cell-based therapies for the nervous system repair.
Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases

Chocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and widespread pathogens. A panel of 148 improved cacao clones was assembled based on productivity and disease resistance, and phenotypic single-tree replicated clonal evaluation was performed for 8 years. Using high-density markers, the diversity of clones was expressed relative to 10 known ancestral cacao populations, and significant effects of ancestry were observed in productivity and disease resistance. Genome-wide association (GWA) was performed, and six markers were significantly associated with frosty pod disease resistance. In addition, genomic selection was performed, and consistent with the observed extensive linkage disequilibrium, high predictive ability was observed at low marker densities for all traits. Finally, quantitative trait locus mapping and differential expression analysis of two cultivars with contrasting disease phenotypes were performed to identify genes underlying frosty pod disease resistance, identifying a significant quantitative trait locus and 35 differentially expressed genes using two independent differential expression analyses. These results indicate that in breeding populations of heterozygous and recently admixed individuals, mapping approaches can be used for low complexity traits like pod color cacao, or in other species single gene disease resistance, however genomic selection for quantitative traits remains highly effective relative to mapping. Our results can help guide the breeding process for sustainable improved cacao productivity.
HEp-2 Cell Adherence, Actin Aggregation, and Intimin Types of Attaching and Effacing Escherichia coli Strains Isolated from Healthy Infants in Germany and Australia

ABSTRACT Fecal samples from healthy children under 2 years of age living in Berlin, Germany (205 infants), and Melbourne, Australia (184 infants), were investigated for the presence of attaching and effacing (AE) Escherichia coli (AEEC) strains by screening for eae (intimin) genes. Twenty-seven AEEC strains were isolated from 14 children (7.6%) from Melbourne and from 12 children (5.9%) from Berlin. The 27 AEEC strains were classified as enterohemorrhagic E. coli (one strain, producing Shiga toxin 1), typical enteropathogenic E. coli (EPEC) (one strain carrying an EPEC adherence factor [EAF] plasmid), and atypical EPEC (25 strains negative for Shiga toxins and EAF plasmids). The AEEC were divided into 18 different serotypes, O-nontypeable and O-rough strains. Typing of their intimin genes revealed the presence of intimin α in 6 strains, intimin β in 11 strains, intimin γ in 7 strains, intimin ζ in 2 strains, and intimin η in one strain. Analysis of HEp-2 cell adherence showed diffuse adherence or localized adherence-like patterns in 26 AEEC strains; local adherence was found only with the EAF-positive strain. Ten AEEC strains showed an AE property with the fluorescent actin staining (FAS) test. The introduction of an EAF plasmid (pMAR7) converted 11 FAS-negative AEEC strains to FAS positive and increased the FAS reaction in six FAS-positive AEEC strains, indicating that the genes needed for the AE phenotype were functional in these strains. Our finding indicates that atypical EPEC strains could play a double role as strains that naturally immunize against intimin in humans and as reservoirs for new emerging human pathogenic EPEC strains.
Attention and engagement-awareness in the wild: A large-scale study with adaptive notifications

In today's advancing ubiquitous computing age, with its ever-increasing amount of information from various applications and services available for consumption, the management of people's attention has become very important. In particular, the high volume of notifications on mobile devices has become a major cause of interruption of users. There has been much research aimed at detecting the opportune moment to present such information to users with in a way that lowers the cognitive load or frustration. However, evaluation of such systems in the real-world production environment with real users and notifications, and evaluation on user's engagement to the presented notification beyond simple responsiveness have not been adequately studied. To the best of our knowledge, this study is the first to investigate user interruptibility and engagement using a real-world large-scale mobile application and real-world notifications consisting of actual news content. We equipped the Yahoo! JAPAN Android app, one of the most popular applications on the national market, with our mobile-sensing and machine-learning-based interruptibility estimation logic. We conducted a large-scale in-the-wild user study with more than 680,000 users for three weeks. The results show that in most cases delaying the notification delivery until an interruptible moment is detected is beneficial to users and results in significant reduction of user response time (49.7%) compared to delivering the notifications immediately. We also observed a higher number of notifications opened in our system as well as constant improvement in user engagement levels throughout the entire study period.
Investigation of the effects of folate deficiency on embryonic development through the establishment of a folate deficient mouse model.

BACKGROUND Folic acid (FA) has been shown to reduce the incidence of neural tube, craniofacial, and cardiovascular defects and low birth weight. The mechanism(s) by which the vitamin is effective, however, has not been determined. Therefore, a folic acid deficient mouse model was developed. METHODS To create a folic acid deficiency, ICR female mice were placed on a diet containing no FA and including 1% succinyl sulfathiazole (SS) for 4 weeks before mating. Control mice were fed diets with either: 1) FA and 1% SS [+SS only diet]; 2) FA [normal diet]; or 3) a breeding diet. Dams and fetuses were examined during various days of gestation. RESULTS Blood analysis showed that by gestational day 18, plasma folate concentrations in the -FA+SS fed dams decreased to 1.13 ng/ml, a concentration approximately 3% of that in breeding diet fed dams (33.24 ng/ml) and 8% of that in +SS only/normal fed dams (13.59 ng/ml). RBC folate levels showed a similar decrease, whereas homocysteine concentrations increased. Reproductive outcome in the -FA+SS fed dams was poor with increased fetal deaths, decreased fetal weight, and delays in palate and heart development. CONCLUSIONS Female mice fed a folic acid deficient diet and 1% succinyl sulfathiazole exhibited many of the characteristics common to human folic acid deficiency, including decreased plasma and RBC folate, increased plasma homocysteine, and poor reproductive outcomes. Thus, an excellent model has been created to investigate the mechanism(s) underlying the origin of birth defects related to folic acid deficiency.
The Barrow Ruptured Aneurysm Trial: 3-year results.

OBJECT The authors report the 3-year results of the Barrow Ruptured Aneurysm Trial (BRAT). The objective of this ongoing randomized trial is to compare the safety and efficacy of microsurgical clip occlusion and endovascular coil embolization for the treatment of acutely ruptured cerebral aneurysms and to compare functional outcomes based on clinical and angiographic data. The 1-year results have been previously reported. METHODS Two-hundred thirty-eight patients were assigned to clip occlusion and 233 to coil embolization. There were no anatomical exclusions. Crossovers were allowed based on the treating physician's determination, but primary outcome analysis was based on the initial assignment to treatment modality. Patient outcomes were assessed independently using the modified Rankin Scale (mRS). A poor outcome was defined as an mRS score>2. At 3 years' follow-up 349 patients who had actually undergone treatment were available for evaluation. Of the 170 patients who had been originally assigned to coiling, 64 (38%) crossed over to clipping, whereas 4 (2%) of 179 patients assigned to surgery crossed over to clipping. RESULTS The risk of a poor outcome in patients assigned to clipping compared with those assigned to coiling (35.8% vs 30%) had decreased from that observed at 1 year and was no longer significant (OR 1.30, 95% CI 0.83-2.04, p=0.25). In addition, the degree of aneurysm obliteration (p=0.0001), rate of aneurysm recurrence (p=0.01), and rate of retreatment (p=0.01) were significantly better in the group treated with clipping compared with the group treated with coiling. When outcomes were analyzed based on aneurysm location (anterior circulation, n=339; posterior circulation, n=69), there was no significant difference in the outcomes of anterior circulation aneurysms between the 2 assigned groups across time points (at discharge, 6 months, 1 year, or 3 years after treatment). The outcomes of posterior circulation aneurysms were significantly better in the coil group than in the clip group after the 1st year of follow-up, and this difference persisted after 3 years of follow-up. However, while aneurysms in the anterior circulation were well matched in their anatomical location between the 2 treatment arms, this was not the case in the posterior circulation where, for example, 18 of 21 posterior inferior cerebellar artery aneurysms were in the clip group. CONCLUSIONS Based on mRS scores at 3 years, the outcomes of all patients assigned to coil embolization showed a favorable 5.8% absolute difference compared with outcomes of those assigned to clip occlusion, although this difference did not reach statistical significance (p=0.25). Patients in the clip group had a significantly higher degree of aneurysm obliteration and a significantly lower rate of recurrence and retreatment. In post hoc analysis examining only anterior circulation aneurysms, no outcome difference between the 2 treatment cohorts was observed at any recorded time point. CLINICAL TRIAL REGISTRATION NO.: NCT01593267 ( ClinicalTrials.gov ).