Miracle-dz/UniFAR-FTUs huggingface dataset:
Different Inducibility of Expression of the Two Xylanase Genes xyn1 and xyn2 in Trichoderma reesei*

Regulation of formation of the extracellular xylanase system of Trichoderma reesei QM 9414 during growth on xylan, cellulose, and replacement onto a number of soluble inducers was investigated by Northern analysis of xyn1 and xyn2 transcripts and by the use of the Escherichia coli hph (hygromycin B-phosphotransferase-encoding) gene as a reporter. Whereas the xyn1 promoter is active in the presence of xylan and xylose, and virtually silenced in the presence of glucose, the xyn2 promoter enables basal transcription at a low level, but is enhanced in the presence of xylan and xylobiose and also of sophorose or cellobiose. The respective regulatory nucleotide regions were localized on a 221-base pair fragment and a 55-base pair fragment of the xyn1 and xyn2 5′-upstream noncoding sequences, respectively. Electrophoretic mobility shift assays, using cell-free extracts, identified induction-specific protein-DNA complexes: one complex of high mobility was observed under basal, noninduced conditions (glucose) with xyn2, which was in part replaced by a slow-migrating complex upon induction by xylan or sophorose. Both complexes bound to a CCAAT box. With xyn1, the induced complex also binds to a CCAAT box, but this binding is not observed in the presence of the carbon catabolite repressor Cre1, which binds to a nearby located consensus motif.
Antibody response to IgA-binding streptococcal M proteins in children with IgA nephropathy.

BACKGROUND IgA nephropathy (IgAN), the most common glomerulonephritis worldwide, is characterized by mesangial deposits containing predominantly IgA. IgAN commonly occurs or exacerbates after upper respiratory tract infections such as streptococcal pharyngitis. Certain group A streptococci express M proteins with IgA-binding regions (IgA-BRs). We have previously shown that these IgA-BRs co-localize with mesangial IgA in IgAN. METHODS Blood samples from patients with IgAN (n = 21) and age-matched controls (n = 83) were assayed by ELISA to detect an IgG antibody response to the IgA-BRs of the M4, M22 and M60 proteins. Antibodies were assayed for each IgA-BR separately and the results were combined. RESULTS Antibody levels to the IgA-BRs were significantly higher in IgAN patients than controls (P = 0.016), particularly in patients with recent streptococcal infection (P = 0.008). Conclusions. The results suggest that children with IgAN had a previous infection with a streptococcal strain expressing an IgA-binding M protein.
Histometric analysis of alveolar bone regeneration with expanded polytetrafluoroethylene (e-PTFE) and latex membranes

Aim: To investigate the amount of connective tissue migrated into the extraction socket using EPTFE and latex membranes. Methods: Seventeen rats were selected and randomly divided into 3 groups: e-PTFE membrane (n = 6), Latex membrane (n = 6) and Control (no membrane, n=5). After extraction of the maxillary right incisor, the animals of the test groups were subjected to alveolar guided bone regeneration (GBR) surgery and received an expanded polytetrafluoroethylene (e-PTFE) and a latex membrane, respectively. Thirty days after surgery, the animals were killed and histometric analysis was done to evaluate the migration of connective tissue. Data were analyzed statistically by one-way ANOVA and multiple-comparison Tukey’s test at 5% significance level. Results: There was statistically significant difference between groups ePTFE and Latex (p=0.001), and between groups e-PTFE and Control (p=0.012), but no significant difference was found between groups Latex and Control (p=0.416). Conclusions: The ePTFE membrane showed better results and appeared more adequate for GBR therapy, forming a barrier to prevent the migration of connective tissue into the extraction socket. The latex membrane, on the other hand, did not show benefits over the control group.
Psychometric properties of the Fatigue Assessment Scale (FAS) in women with breast problems

To examine the usefulness of the Fatigue Assessment Scale (FAS) in women with benign breast problems (BBP) and women with early stage breast cancer (BC). Women with a palpable lump in the breast or an abnormality on a screening mammography (N = 560) completed the FAS (four time points) and measures of anxiety, depressive symptoms, neuroticism, and fatigue. The FAS appeared to have a good fit in the total population (Comparative Fit Index (CFI) = . 96; × 2 (29) = 104.5; p < . 001; Nonnormed Fit Index (NNFI) = . 95; Root Mean Square Error of Approximation (RMSEA) = . 091), the BC group (CFI = .95; X 2 (32) = 69.6, p < . 001; NNFI = . 91; RMSEA = . 090), and the BBP group (CFI = .95; × 2 (34) = 99.9, p < . 001; NNFI = . 92; RMSEA = . 105). The internal consistency (.89 total group) and the test-retest reliability (BBP group; r = .88 three months interval) were good. The FAS was a distinct factor from depressive symptoms, neuroticism, and state anxiety. In conclusion, the FAS has good reliability and validity in women with breast problems and measures fatigue without substantial overlap with depressive symptoms, state anxiety, and neuroticism.
Farnesyl Transferase Inhibitors Block the Farnesylation of CENP-E and CENP-F and Alter the Association of CENP-E with the Microtubules*

Human tumor cell lines that are sensitive to the effects of farnesyl transferase inhibitors accumulate in G2 → M (except for cells with an activated Ha-ras that accumulate in G1). A search for CAAX box proteins from Swiss-Prot revealed more than 300 peptides. Of these, the centromeric proteins CENP-E and CENP-F are preferentially expressed during mitosis and are implicated as mediators of the G2 → M checkpoint. Experiments performed here show that peptides from the COOH-terminal CAAX box of CENP-E and CENP-F are substrates for farnesyl transferase but not geranylgeranyl transferase-I. Although both proteins are prenylated in the human tumor cell line DLD-1, their prenylation is completely inhibited by the farnesyl transferase inhibitor, SCH 66336. Immunohistochemical data with the lung carcinoma cell line, A549, showed that preventing the farnesylation of CENP-E and CENP-F by treatment with the farnesyl transferase inhibitor SCH 66336 does not affect their localization to the kinetochores. However, the presence of farnesyl transferase inhibitors alters the association between CENP-E and the microtubules. Our results imply that the inhibition of CENP-E farnesylation results in the alteration of the microtubule-centromere interaction during mitosis and results in the accumulation of cells prior to metaphase.
Perseveration on place reversals in spatial swimming pool tasks: Further evidence for place learning in hippocampal rats

Animals with damage to the fimbria–fornix (FF) or cells of the hippocampus (HIP) can learn a place problem but cannot learn matching‐to‐place problems, which feature a series of place “reversals. ” The two experiments described in the present report were designed to examine the causes of impairment on reversal learning. In experiment 1, control, HIP, and FF groups were trained to asymptote on a place problem, and then the location of the platform was moved. Control rats learned the reversal response more quickly than the initial response; the HIP rats learned both problems at the same rate. Swim analysis showed that the impairment in the lesion group on the reversal response was aggravated by perseverative returns to the first learned place. In experiment 2, control and FF groups were trained on a task in which the platform was visible on three daily trials and hidden on one daily trial. After 10 days, the platforms were moved. In the reversal response, the FF group showed enhanced performance on the cue trials and severely impaired performance on the place trials relative to initial learning and control performance. Swim analysis showed that FF rats perseverated on the initial place response in place trials. These experiments provide further evidence for place learning in hippocampal rats and show that perseverative responses contribute to impairments in new learning. The results are discussed in relation to the idea that the hippocampus mediates spatial mapping and/or uses self‐movement cues to solve spatial problems. Hippocampus 7:361–370, 1997. © 1997 Wiley‐Liss, Inc.
Mutation Analysis of IDH1 in Paired Gliomas Revealed IDH1 Mutation Was Not Associated with Malignant Progression but Predicted Longer Survival

Recurrence and progression to higher grade lesions are characteristic behaviorsof gliomas. Though IDH1 mutation frequently occurs and is considered as an early event in gliomagenesis, little is known about its role in the recurrence and progression of gliomas. We therefore analysed IDH1 and IDH2 statusat codon 132 of IDH1 and codon 172 of IDH2 by direct sequencing and anti-IDH1-R132H immunohistochemistry in 53 paired samples and their recurrences, including 29 low- grade gliomas, 16 anaplastic gliomas and 8 Glioblastomas. IDH1/IDH2 mutation was detected in 32 primarytumors, with 25 low- grade gliomas and 6 anaplastic gliomas harboring IDH1 mutation and 1 low- grade glioma harboring IDH2 mutation. All of the paired tumors showed consistent IDH1 and IDH2 status. Patients were analyzed according to IDH1 status and tumor-related factors. Malignant progression at recurrence was noted in 22 gliomas and was not associated with IDH1 mutation. Survival analysis revealed patients with IDH1 mutated gliomas had a significantly longer progression-free survival (PFS) and overall survival (OS). In conclusion, this study demonstrated a strong tendency of IDH1/IDH2 status being consistent during progression of glioma. IDH1 mutation was not a predictive marker for malignant progression and it was a potential prognostic marker for gliomas of Chinese patients.
A double blind, randomised, controlled trial of glutamine supplementation in parenteral nutrition

BACKGROUND AND AIMS To determine whether the inclusion of 20 g free glutamine as part of the nitrogen source of parenteral feeds reduces length of hospital stay or mortality. METHODS In a randomised, double blind, controlled trial in 168 patients clinically accepted for parenteral nutrition, standard feeds were compared with feeds in which 3.8 g of the total nitrogen was replaced with the equivalent 20 g glutamine. A minimum of 11 g nitrogen/day was used in all patients. Daily intakes of energy and nitrogen were determined using a validated computer protocol and were similar for the two groups. All feeds included trace elements, vitamins, electrolytes, and minerals. RESULTS A total of 85 patients received a median of eight (interquartile range 5–13) daily feeds containing glutamine while 83 received a median of eight (5–15) standard feeds. No difference between groups was detected for infective complications. Twenty control patients and 14 who had received glutamine died during their hospital stay (NS). Median length of stay was 32 (23–52) days on glutamine, which was not significantly different from the control value of 35 (25–55) days. Glutamine was associated with a significant (p<0.03) reduction in length of stay in surgical patients (45 days (range 29–81) versus 30 days (range 19–54)). CONCLUSION The benefit from glutamine supplementation of parenteral feeds as used in this trial has not been proved. Supplementation may have advantages in surgical patients and in haematological malignancy. Further trials are required.
Robot ’ s Slip of the Tongue : Effect of Speech Error on the Familiarity of a Humanoid Robot Author

This study investigated the effect of speech errors made by a robot on people’s perception of the familiarity of the robot. Four types of speech errors were implemented for a communicating robot. Subjects’ perception of the familiarity of the robot, along with other subjective evaluations of impressions of the robot, were measured in an experiment and compared between conditions with and without speech error. Results showed that speech error improved the familiarity score when the robot did not make any speech errors in the first contact with subjects and then made speech errors in the second contact on a separate day. On the other hand, speech errors lowered people’s perception of the sincerity of the robot. These results imply that the robot should not make speech errors in the early stage of engagement with human users, while some speech errors after the users become accustomed with the robot might be effective in improving users’ perception of the familiarity of the robot. Results also showed that speech error improved familiarity for people having low-scoring attitudes about the diversity and operation of robots.
An Optimal Algorithm for Relay Node Assignment in Cooperative Ad Hoc Networks

Recently, cooperative communications, in the form of having each node equipped with a single antenna and exploit spatial diversity via some relay node's antenna, is shown to be a promising approach to increase data rates in wireless networks. Under this communication paradigm, the choice of a relay node (among a set of available relay nodes) is critical in the overall network performance. In this paper, we study the relay node assignment problem in a cooperative ad hoc network environment, where multiple source-destination pairs compete for the same pool of relay nodes in the network. Our objective is to assign the available relay nodes to different source-destination pairs so as to maximize the minimum data rate among all pairs. The main contribution of this paper is the development of an optimal polynomial time algorithm, called ORA, that achieves this objective. A novel idea in this algorithm is a “linear marking” mechanism, which maintains linear complexity of each iteration. We give a formal proof of optimality for ORA and use numerical results to demonstrate its capability.
Structural and Functional Basis for p38-MK2-Activated Rsk Signaling in Toll-Like Receptor-Stimulated Dendritic Cells

ABSTRACT Rsk kinases play important roles in several cellular processes such as proliferation, metabolism, and migration. Until recently, Rsk activation was thought to be exclusively initiated by Erk1/2, but in dendritic cells (DC) Rsk is also activated by p38 mitogen-activated protein (MAP) kinase via its downstream substrates, MK2/3. How and why this noncanonical configuration of the MAP kinase pathway is adopted by these key immune cells are not known. We demonstrate that the Erk1/2-activated C-terminal kinase domain of Rsk is dispensable for p38-MK2/3 activation and show that compared with fibroblasts, a greater fraction of p38 and MK2/3 is located in the cytosol of DC prior to stimulation, suggesting a partial explanation for the operation of the noncanonical pathway of Rsk activation in these cells. p38/MK2/3-activated Rsk phosphorylated downstream targets and is physiologically important because in plasmacytoid DC (pDC) stimulated with Toll-like receptor 7 (TLR7) agonists, Erk1/2 activation is very weak relative to p38. As a result, Rsk activation is entirely p38 dependent. We show that this unusual configuration of MAP kinase signaling contributes substantially to production of type I interferons, a hallmark of pDC activation.
Cost-effectiveness of noninvasive ventilation for chronic obstructive pulmonary disease-related respiratory failure in Indian hospitals without ICU facilities

Introduction: The majority of Indian hospitals do not provide intensive care unit (ICU) care or ward-based noninvasive positive pressure ventilation (NIV). Because no mechanical ventilation or NIV is available in these hospitals, the majority of patients suffering from respiratory failure die. Objective: To perform a cost-effective analysis of two strategies (ward-based NIV with concurrent standard treatment vs standard treatment alone) in chronic obstructive pulmonary disease (COPD) respiratory failure patients treated in Indian hospitals without ICU care. Materials and Methods: A decision-analytical model was created to compare the cost-effectiveness for the two strategies. Estimates from the literature were used for parameters in the model. Future costs were discounted at 3%. All costs were reported in USD (2012). One-way, two-way, and probabilistic sensitivity analysis were performed. The time horizon was lifetime and perspective was societal. Results: The NIV strategy resulted in 17.7% more survival and was slightly more costly (increased cost of $101 (USD 2012) but resulted in increased quality-adjusted life-years (QALYs) (1.67 QALY). The cost-effectiveness (2012 USD)/QALY in the standard and NIV groups was $78/QALY ($535.02/6.82) and $75/QALY ($636.33/8.49), respectively. Incremental cost-effectiveness ratio (ICER) was only $61 USD/QALY. This was substantially lower than the gross domestic product (GDP) per capita for India (1489 USD), suggesting the NIV strategy was very cost effective. Using a 5% discount rate resulted in only minimally different results. Probabilistic analysis suggests that NIV strategy was preferred 100% of the time when willingness to pay was >$250 2012 USD. Conclusion: Ward-based NIV treatment is cost-effective in India, and may increase survival of patients with COPD respiratory failure when ICU is not available.
Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary

Tidal flats are soil resources of great significance. Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. We determined the abundance as well as composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in different soils during land reclamation process. The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction (PCR). The different abundances of AOB and AOA were negatively correlated with the salinity. The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene. Among AOB, nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process, i.e., tidal flats, while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process, farm land and wild land. The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate. As for AOA, there was no obvious correlation with the changes in the physicochemical properties of the soil. This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages.
Human Analogue of the Morris Water Maze for Testing Subjects at Risk of Alzheimer’s Disease

Background: Patients with Alzheimer’s disease (AD) and amnestic mild cognitive impairment (MCI) have difficulties with spatial orientation. Objective: To test hypothesis that spatial navigation is impaired early in MCI patients representing the presymptomatic stage of AD. Methods: We tested patients with probable AD (n = 21), MCI, further classified according to Petersen’s criteria as amnestic MCI (aMCI) single domain (n = 11), aMCI multiple domain (n = 31), or nonamnestic MCI (n = 7). The aMCI group was also stratified using cued recall according to Dubois’ criteria into memory impairment of the hippocampal type (n = 10) and isolated memory retrieval impairment-nonhippocampal (n = 32) and also according to ApoE4 status into E4+ (n = 12) and E4– (n = 30). These patients and controls (n = 28) were tested in the human variant of the Morris water maze. Depending on the subtest, the subjects could use the egocentric or allocentric (hippocampus-dependent) navigation. Results: The AD and aMCI multiple domain groups were impaired in all subtests. The aMCI single domain group was impaired in allocentric subtests. The hippocampal MCI group performed poorer than the nonhippocampal MCI group and similarly to the AD group. The ApoE4+ group was as bad as the AD group when compared with the E4– group. Conclusion: aMCI subjects represent a very heterogeneous population, and spatial memory or cued recall examination can add more value to aMCI classification. ApoE4+ patients are more impaired than ApoE4– patients.
Frequency-Specific Relation between Hippocampal Theta Rhythm, Behavior, and Amobarbital Action

The frequency of the hippocampal theta rhythm in freely moving rats varies predictably in relation to behavior in a simple learning situation. The theta rhythm may be driven by electrical stimulation of the medial septal area at frequencies within the theta range. The threshold for septal driving is lowest at that frequency which the rat displays in response to frustrative nonreward; the driving threshold is selectively raised at this frequency by sodium amobarbital. It is suggested that the behavioral effects of amobarbital are due to a disruption of the theta frequency normally displayed in response to nonreward.
Mechanism of cytotoxicity induced by chimeric mouse human monoclonal antibody IDEC-C2B8 in CD20-expressing lymphoma cell lines.

With a new flow cytometric cytotoxicity assay, we examined the mechanism of action of chimeric mouse human anti-CD20 monoclonal antibody IDEC-C2B8. IDEC-C2B8 alone induced direct cytotoxicity in four of eight examined CD20-expressing lymphoma cell lines (RAJI, DAUDI, JOK-1, and WT100) at a concentration above 100 ng/ml. Moreover, after 4 h incubation in human serum, only a moderate complement-dependent cellular cytotoxicity (CDCC) was observed, whereas cytotoxicity increased markedly after 3 days of culture, indicating that combined direct cytotoxicity and CDCC were responsible. IDEC-C2B8 induced an effective antibody-dependent cellular cytotoxicity (ADCC) in seven of eight tested lymphoma cell lines when peripheral blood mononuclear cells were used as effector cells. ADCC was moderately enhanced by cytokine interleukin-2, whereas interleukin-12, interferon-alpha, and GM-CSF had no influence. Interestingly, we could demonstrate a correlation between CD32 expression on lymphoma cell lines and IDEC-C2B8-induced direct cytotoxicity, indicating that crosslinking of CD20 with CD32 may be involved in the mechanism of cytotoxicity. We propose that direct cytotoxicity, CDCC, and ADCC result in the marked elimination of CD20-expressing tumor cells observed after treatment with IDEC-C2B8.
Strict-sense constrained Markov decision processes

We introduce the strict-sense constrained Markov decision processes by extending the ideas of classical constrained Markov decision process and the safety control of discrete event systems. In our setting a convex set of constraint specified by a set of linear inequalities is given for the system's state probability distribution. A distribution is safe if it is in the set of constraint. A policy is safe if it makes a state distribution that is initially safe remain safe after the process starts. Under the assumption of complete state observation, we first identify the optimal safe policy that minimizes the pre-specified cost function. Then, for a given safe policy, we provide an iterative algorithm for computing the maximum set of safe initial distributions corresponding to the policy. Under the assumption that the policy induces a unique limiting distribution in the interior of set of constraint, we give an explicit upper bound on the number of steps needed for the termination of the algorithm. In particular, we give the explicit expression for the maximum set of safe initial distributions in the two-state system, for which we show that at most one iteration is needed in running the algorithm