Miracle-dz/UniFAR-FTUs huggingface dataset:
Diet-Dependent Shifts in the Bacterial Population of the Rumen Revealed with Real-Time PCR

ABSTRACT A set of PCR primers was designed and validated for specific detection and quantification of Prevotella ruminicola,Prevotella albensis, Prevotella bryantii,Fibrobacter succinogenes, Selenomonas ruminantium-Mitsuokella multiacida, Streptococcus bovis, Ruminococcus flavefaciens,Ruminobacter amylophilus, Eubacterium ruminantium, Treponema bryantii,Succinivibrio dextrinosolvens, and Anaerovibrio lipolytica. By using these primers and the real-time PCR technique, the corresponding species in the rumens of cows for which the diet was switched from hay to grain were quantitatively monitored. The dynamics of two fibrolytic bacteria, F. succinogenesand R. flavefaciens, were in agreement with those of earlier, culture-based experiments. The quantity of F. succinogenes DNA, predominant in animals on the hay diet, fell 20-fold on the third day of the switch to a grain diet and further declined on day 28, with a 57-fold reduction in DNA. TheR. flavefaciens DNA concentration on day 3 declined to approximately 10% of its initial value in animals on the hay diet and remained at this level on day 28. During the transition period (day 3), the quantities of two ruminal prevotella DNAs increased considerably: that of P. ruminicola increased 7-fold and that ofP. bryantii increased 263-fold. On day 28, the quantity of P. ruminicola DNA decreased 3-fold, while P. bryantii DNA was still elevated 10-fold in comparison with the level found in animals on the initial hay diet. The DNA specific for another xylanolytic bacterium, E. ruminantium, dropped 14-fold during the diet switch and was maintained at this level on day 28. The concentration of a rumen spirochete, T. bryantii, decreased less profoundly and stabilized with a sevenfold decline by day 28. The variations in A. lipolytica DNA were not statistically significant. After an initial slight increase in S. dextrinosolvens DNA on day 3, this DNA was not detected at the end of the experiment. S. bovis DNA displayed a 67-fold increase during the transition period on day 3. However, on day 28, it actually declined in comparison with the level in animals on the hay ration. The amount of S. ruminantium-M. multiacida DNA also increased eightfold following the diet switch, but stabilized with only a twofold increase on day 28. The real-time PCR technique also uncovered differential amplification of rumen bacterial templates with the set of universal bacterial primers. This observation may explain why some predominant rumen bacteria have not been detected in PCR-generated 16S ribosomal DNA libraries.
Patterns of Histone H3 Lysine 27 Monomethylation and Erythroid Cell Type-specific Gene Expression*

Post-translational histone modifications, acting alone or in a context-dependent manner, influence numerous cellular processes via their regulation of gene expression. Monomethylation of histone H3 lysine 27 (K27me1) is a poorly understood histone modification. Some reports describe depletion of K27Me1 at promoters and transcription start sites (TSS), implying its depletion at TSS is necessary for active transcription, while others have associated enrichment of H3K27me1 at TSS with increased levels of mRNA expression. Tissue- and gene-specific patterns of H3K27me1 enrichment and their correlation with gene expression were determined via chromatin immunoprecipitation on chip microarray (ChIP-chip) and human mRNA expression array analyses. Results from erythroid cells were compared with those in neural and muscle cells. H3K27me1 enrichment varied depending on levels of cell-type specific gene expression, with highest enrichment over transcriptionally active genes. Over individual genes, the highest levels of H3K27me1 enrichment were found over the gene bodies of highly expressed genes. In contrast to H3K4me3, which was highly enriched at the TSS of actively transcribing genes, H3K27me1 was selectively depleted at the TSS of actively transcribed genes. There was markedly decreased to no H3K27me1 enrichment in genes with low expression. At some locations, H3K27 monomethylation was also found to be associated with chromatin signatures of gene enhancers.
An Aminopeptidase from Mouse Brain Cytosol That Cleaves N‐Terminal Acidic Amino Acid Residues

An aminopeptidase with specificity directed toward peptides with acidic N‐terminal amino acid residues has been isolated from mouse brain cytosol. Purification by ion‐exchange chromatography and gel filtration resulted in an enzyme that hydrolyzed aspartyl‐phenylala‐nine methyl ester at a rate of 13.2 μu,mol/min/mg protein at pH 7.5, an increase in specific activity of 1000‐fold over that of brain homogenate. Its apparent molecular weight, determined by gel filtration, is ˜450,000. Dipeptides with N‐terminal aspartyl residues are cleaved preferentially to glutamic‐containing analogs, and a neutral amino acid (or histidine) is necessary in the adjacent position. For pep‐tides of the form aspartyl‐X, relative activity was 100, 81, 71, 66, 19, or 0, where X was alanine, serine, leucine, phenylalanine, histidine, or proline, respectively. Tripep‐tides were more rapidly hydrolyzed than dipeptides; however, activity tended to decline with increasing chain length. The acidic aminopeptidase can account for almost all of the activity of brain cytosol toward the N‐terminal aspartyl residue of angiotensin II, aspartyl‐phenylalanine methyl ester or aspartyl‐alanine, and the N‐terminal glu‐tamyl residue of adrenocorticotropin(5‐10). The enzyme was unaffected by bestatin or amastatin. It was inhibited by o‐phenanthroline and EDTA. The latter effect could be reversed completely by Zn2+ and partially by Mn2+ or Mg2+; Co2+ and Fe2+ had no effect; Ca2+ was inhibitory. These properties distinguish the brain acidic aminopeptidase from aminopeptidase A isolated from human serum or pig kidney and the aspartyl aminopeptidase of dog kidney.
Coverage of apple surface for adequate machine vision inspection

Automated inspection of apples requires that the entire surface of the fruit passes through the view of at least one camera. This work uses Monte Carlo simulation to investigate the extent of coverage of the apple surface when viewed by three four and five cameras arranged in a plane. Each camera has a circular inspection area that is 45 to 50% of the apple size. The number of images per apple rotation and the level of asymmetry (or drunkenness) of the apple's roll are varied to determine their effect on the extent of surface coverage. Results for a single rotation of the apple show that complete surface coverage is not possible with three cameras and up to 30 images per rotation. Four cameras can provide complete surface coverage at 30 images per rotation and five cameras can provide complete surface coverage at 15 images per rotation. The greater the extent of surface coverage the greater the redundancy in inspection and the greater the possibility of false positives. However it is likely that several inspections of each defect will provide more secure recognition than that provided by just one sight of the defect. Increase in the drunkenness of the apple roll has a large adverse effect on the extent of surface coverage and redundancy.
Color Doppler imaging in untreated high- and normal-pressure open-angle glaucoma.

PURPOSE To evaluate ocular blood flow velocity indices in untreated primary open-angle glaucoma (POAG) and normal pressure glaucoma (NPG). METHODS Twenty-five untreated patients with NPG, 23 untreated patients with POAG, and 26 age-matched normal control subjects underwent color Doppler imaging for the measurement of blood flow velocity in the central retinal and ophthalmic arteries. Neither the patients nor the control subjects were using systemic beta-blockers or calcium channel blockers. After log transformation of non-normal data, group differences were compared with a one-way analysis of variance followed by unpaired t-test with the Bonferroni correction. Statistical significance was set at P < 0.05. RESULTS The central retinal artery end diastolic velocity was significantly lower in patients with POAG than in normal subjects. The ophthalmic artery peak systolic velocity (PSV) was significantly greater in patients with POAG than in those with NPG and normal subjects. The resistance index (RI) of both the ophthalmic and central retinal arteries was significantly greater in patients with POAG than in normal subjects, and the central retinal artery RI was significantly greater in those with NPG than in normal subjects. Systemic pulse pressure and systolic blood pressure were significantly greater in patients with POAG compared with normal subjects. Multiple regression analysis showed a significant relation between ophthalmic artery PSV and intraocular pressure (but not with any of the cardiovascular parameters) in the POAG group. Chi-square analysis found significantly more systemic vascular disease in patients with NPG and POAG compared with that of normal subjects. CONCLUSIONS There was an increased resistance to blood flow in the central retinal artery of untreated patients with NPG and POAG and also in the ophthalmic artery of patients with POAG. The ophthalmic artery peak systolic velocity was elevated in untreated patients with POAG. Altered ocular circulation (with different patterns of presentation) appears to be common to patients with NPG and patients with POAG.
Altered expression of the transcription factor Mef2c during retinal degeneration in Rpe65-/- mice.

PURPOSE To investigate the role of the myocyte enhancer factor 2 (Mef2) transcription factor family in retinal diseases, Mef2c expression was assessed during retinal degeneration in the Rpe65(-/-) mouse model of Leber's congenital amaurosis (LCA). Mef2c-dependent expression of photoreceptor-specific genes was further addressed. METHODS Expression of Mef2 members was analyzed by oligonucleotide microarray, quantitative PCR (qPCR), and in situ hybridization. Mef2c-dependent transcriptional activity was assayed by luciferase assay in HEK293T cells. RESULTS Mef2c was the only Mef2 member markedly downregulated during retinal degeneration in Rpe65(-/-) mice. Mef2c mRNA level was decreased by more than 2-fold at 2 and 4 months and by 3.5-fold at 6 months in retinas of Rpe65(-/-) mice. Downregulation of Mef2c at the protein level was confirmed in Rpe65(-/-) retinas. The decrease in Mef2c mRNA levels in the developing Rpe65(-/-) retinas from postnatal day (P) 13 onward was concomitant with the decreased expression of the rod-specific transcription factors Nrl and Nr2e3. Nrl was further shown to drive Mef2c transcriptional activity, supporting a physiological role for Mef2c in the retina. In addition, Mef2c appeared to act as a transcriptional repressor of its own expression and the expression of the retina-specific retinal G-protein coupled receptor (Rgr), rhodopsin, and M-opsin genes. CONCLUSIONS These findings highlight the early altered regulation of the rod-specific transcriptional network in Rpe65-related disease. They also indicate that Mef2c may act as a novel transcription factor involved in the development and the maintenance of photoreceptor cells.
Surface-Dried Viruses Can Resist Glucoprotamin-Based Disinfection

ABSTRACT Touching of contaminated objects and surfaces is a well-known method of virus transmission. Once they are attached to the hands, viruses can easily get adsorbed and initiate infection. Hence, disinfection of frequently touched surfaces is of major importance to prevent virus spreading. Here we studied the antiviral activity of a glucoprotamin-containing disinfectant against influenza A virus and the model virus vaccinia virus (VACV) dried on inanimate surfaces. The efficacy of the surface disinfectant on stainless steel, polyvinyl chloride, and glass coupons was investigated in a quantitative carrier test. Vacuum-dried viruses were exposed to 0.25%, 0.5%, and 1% disinfectant for 5 min, 15 min, and 30 min without agitation, and residual infectivity was determined by endpoint titration. Although glucoprotamin was highly active against both viruses in suspension, limited antiviral activity against the surface-dried viruses was detected. Even after 30 min of exposure to 1% disinfectant, VACV was not completely inactivated. Furthermore, influenza A virus inactivation was strongly affected by the surface composition during the 5-min and 15-min treatments with 0.25% and 0.5% disinfectant. The results presented in this study highlight the relevance of practical tests to assess the antiviral activity of surface disinfectants. High virucidal activity in solution is not necessarily indicative of high antiviral activity against surface-dried viruses. In addition, we want to emphasize that the mere exposure of surfaces to disinfectants might not be sufficient for virus inactivation and mechanical action should be applied to bring attached viruses into contact with virucidal compounds.
Combined treatment of tumor-tropic human neural stem cells containing the CD suicide gene effectively targets brain tumors provoking a mild immune response.

Previous studies showed promise of coupling genetically engineered neural stem cells (NSCs) with blood-brain barrier permeable prodrugs as an effective anti-brain tumor therapy. Here, we further advance those findings by testing the suicide gene therapeutic system in syngenic glioblastoma immunocompetent mice. After intracranial injection of HB1.F3.CD, an immortalized human NSC cell line engineered to constitutively produce cytosine deaminase (CD), the prodrug 5-fluorocytosine (5-FC) was administered for five days, q.d. , via intraperitoneal injection. The HB1. F3.CD hNSCs migrated specifically to the brain tumor site via the corpus callosum and significantly reduced the tumor volume (67%) by converting 5-FC into the cytotoxic 5-fluorouracil. A corresponding increase in F4/80-positive population was observed in the treatment group, although CD3-positive population remained unchanged compared to control. No toxic effects or morphological changes were observed in the spleen and the lymph nodes. The data suggest that the NSC-enzyme/prodrug treatment is an effective anti-tumor therapeutic strategy that specifically targets only the tumor site with little or no systemic side effects. In addition, the treatment modeled here successfully elicited a macrophagic immune response which seemed to have a synergistic role in reducing tumor volume, thus showing promise for treatment-mediated enhancement of inherent immune responses against brain tumors.
Tremor dominant parkinsonism: Clinical description and LRRK2 mutation screening

Tremor dominant parkinsonism (TDP) is characterized by initial prominent resting and action tremor, mild parkinsonism, unpredictable response to medication, and a better prognosis than idiopathic Parkinson's disease (PD). We report on clinical features and longitudinal course of 26 patients suffering from TDP. Mean disease duration was 6.5 ± 3 years, 61.5% of patients had a positive family history of tremor, 73% did not need drug treatment, performance of 123I‐Ioflupane SPECT showed reduced striatal tracer uptake in 65.4% of patients, and odor identification testing was pathologic in all the patients tested (n = 22). Co‐occurrence of action and resting tremor were the most annoying and disabling symptoms in all the patients, whereas rigidity and/or bradykinesia were clinically irrelevant in most of them. We also sequenced the full coding region of the Leucine‐rich repeat kinase 2 gene (LRRK2) in all patients. We found a novel Val2390Met mutation that was not found in 864 chromosomes. Our results suggest a broader clinical heterogeneity related to LRRK2 mutations and points towards TDP as a subtype within the spectrum of PD, in which disabling tremor but otherwise mild parkinsonian signs and a better prognosis are the main characteristics. © 2007 Movement Disorder Society
Edg-2/Vzg-1 Couples to the Yeast Pheromone Response Pathway Selectively in Response to Lysophosphatidic Acid*

We have functionally expressed the human cDNA encoding the putative lysophosphatidic acid (LPA) receptor Edg-2 (Vzg-1) in Saccharomyces cerevisiae in an attempt to determine the agonist specificity of this G-protein-coupled receptor. LPA activated the pheromone response pathway in S. cerevisiaeexpressing Edg-2 in a time- and dose-dependent manner as determined by induction of a pheromone-responsiveFUS1::lacZ reporter gene. LPA-mediated activation of the pheromone response pathway was dependent on mutational inactivation of the SST2 gene, the GTPase-activating protein for the yeast Gα protein (the GPA1gene product). This indicates that, in sst2Δ yeast cells, Edg-2 can efficiently couple to the yeast heterotrimeric G-protein in response to LPA and activate the yeast mitogen-activated protein kinase pathway. The Edg-2 receptor showed a high degree of specificity for LPA; other lyso-glycerophospholipids, sphingosine 1-phosphate, and diacyl-glycerophospholipids did not activateFUS1::lacZ. LPA analogs including a cyclic phosphoester form and ether-linked forms of LPA activatedFUS1::lacZ, although fatty acid chains of 6 and 10 carbons did not activate FUS1::lacZ, suggesting a role for the side chain in ligand binding or receptor activation. These results indicate that Edg-2 encodes a highly specific LPA receptor.
Stereo-assisted landmark detection for the analysis of changes in 3-D facial shape

In this paper, a semi-automated approach to 3-D landmark digitization of the face is described which uses a combination of active shape model-driven feature detection and stereophotogrammetric analysis. The study aims to assess whether the proposed method is capable of detecting statistically significant changes in facial soft tissue shape due to mandibular repositioning in a cross-sectional patient sample. A hybrid stereophotogrammetric and structured-light imaging system is used for acquiring 3-D face models in the first instance. A landmark-based statistical analysis of facial shape change is then carried out using procrustes registration, principal component analysis and thin plate spline warping on the 2-D facial midline profiles and automatically digitized 3-D landmarks. The proposed method is validated both statistically and visually by characterizing shape changes induced by mandibular repositioning in a heterogeneous cross-sample of 20 orthodontic patients. It is shown that the method is capable of distinguishing between changes in facial morphology due to simulated surgical correction and changes due to other factors such as growth and normal variation within the patient sample. The study shows that the proposed method may be useful for auditing outcomes of clinical treatment or surgical intervention which result in changes to facial soft tissue morphology.
A low complexity physical-layer network coding scheme for cellular two-way relaying systems

In this paper, we consider transceiver design for multiuser cellular two-way relay network (cTWRC), where a multi-antenna base station (BS) exchanges information with multiple single-antenna mobile stations (MSs) with the help of a multi-antenna relay station (RS). We propose a low complexity two-way relaying scheme for cTWRC via signal space alignment. In our scheme, the precoders at the BS and MSs are jointly designed that the two data streams delivered to and from the same MS fall in the same spatial direction at the RS. With such signal space alignment, interference-free physical-layer network coding can be performed at the relay. We analyze the end-to-end sum bit error rate (BER) performance of the proposed scheme and investigate the optimal power allocation at the BS and RS to improve the BER performance. Numerical results demonstrate that our scheme is superior to the existing amplify-and-forward based signal alignment schemes.
Rational Modification of Ligand‐Binding Preference of Avidin by Circular Permutation and Mutagenesis

Chicken avidin is a key component used in a wide variety of biotechnological applications. Here we present a circularly permuted avidin (cpAvd4→3) that lacks the loop between β‐strands 3 and 4. Importantly, the deletion of the loop has a positive effect on the binding of 4′‐hydroxyazobenzene‐2‐carboxylic acid (HABA) to avidin. To increase the HABA affinity of cpAvd4→3 even further, we mutated asparagine 118 on the bottom of the ligand‐binding pocket to methionine, which simultaneously caused a significant drop in biotin‐binding affinity. The X‐ray structure of cpAvd4→ 3(N118M) allows an understanding of the effect of mutation to biotin‐binding, whereas isothermal titration calorimetry revealed that the relative binding affinity of biotin and HABA had changed by over one billion‐fold between wild‐type avidin and cpAvd4→3(N118M). To demonstrate the versatility of the cpAvd4→3 construct, we have shown that it is possible to link cpAvd4→3 and cpAvd5→4 to form the dual‐chain avidin called dcAvd2. These novel avidins might serve as a basis for the further development of self‐organising nanoscale avidin building blocks.
Pathophysiology of sleep apnea.

Sleep-induced apnea and disordered breathing refers to intermittent, cyclical cessations or reductions of airflow, with or without obstructions of the upper airway (OSA). In the presence of an anatomically compromised, collapsible airway, the sleep-induced loss of compensatory tonic input to the upper airway dilator muscle motor neurons leads to collapse of the pharyngeal airway. In turn, the ability of the sleeping subject to compensate for this airway obstruction will determine the degree of cycling of these events. Several of the classic neurotransmitters and a growing list of neuromodulators have now been identified that contribute to neurochemical regulation of pharyngeal motor neuron activity and airway patency. Limited progress has been made in developing pharmacotherapies with acceptable specificity for the treatment of sleep-induced airway obstruction. We review three types of major long-term sequelae to severe OSA that have been assessed in humans through use of continuous positive airway pressure (CPAP) treatment and in animal models via long-term intermittent hypoxemia (IH): 1) cardiovascular. The evidence is strongest to support daytime systemic hypertension as a consequence of severe OSA, with less conclusive effects on pulmonary hypertension, stroke, coronary artery disease, and cardiac arrhythmias. The underlying mechanisms mediating hypertension include enhanced chemoreceptor sensitivity causing excessive daytime sympathetic vasoconstrictor activity, combined with overproduction of superoxide ion and inflammatory effects on resistance vessels. 2) Insulin sensitivity and homeostasis of glucose regulation are negatively impacted by both intermittent hypoxemia and sleep disruption, but whether these influences of OSA are sufficient, independent of obesity, to contribute significantly to the "metabolic syndrome" remains unsettled. 3) Neurocognitive effects include daytime sleepiness and impaired memory and concentration. These effects reflect hypoxic-induced "neural injury. " We discuss future research into understanding the pathophysiology of sleep apnea as a basis for uncovering newer forms of treatment of both the ventilatory disorder and its multiple sequelae.