Miracle-dz/UniFAR-FTUs huggingface dataset:
CpcM Posttranslationally Methylates Asparagine-71/72 of Phycobiliprotein Beta Subunits in Synechococcus sp. Strain PCC 7002 and Synechocystis sp. Strain PCC 6803

ABSTRACT Cyanobacteria produce phycobilisomes, which are macromolecular light-harvesting complexes mostly assembled from phycobiliproteins. Phycobiliprotein beta subunits contain a highly conserved γ-N-methylasparagine residue, which results from the posttranslational modification of Asn71/72. Through comparative genomic analyses, we identified a gene, denoted cpcM, that (i) encodes a protein with sequence similarity to other S-adenosylmethionine-dependent methyltransferases, (ii) is found in all sequenced cyanobacterial genomes, and (iii) often occurs near genes encoding phycobiliproteins in cyanobacterial genomes. The cpcM genes of Synechococcus sp. strain PCC 7002 and Synechocystis sp. strain PCC 6803 were insertionally inactivated. Mass spectrometric analyses of phycobiliproteins isolated from the mutants confirmed that the CpcB, ApcB, and ApcF were 14 Da lighter than their wild-type counterparts. Trypsin digestion and mass analyses of phycobiliproteins isolated from the mutants showed that tryptic peptides from phycocyanin that included Asn72 were also 14 Da lighter than the equivalent peptides from wild-type strains. Thus, CpcM is the methyltransferase that modifies the amide nitrogen of Asn71/72 of CpcB, ApcB, and ApcF. When cells were grown at low light intensity, the cpcM mutants were phenotypically similar to the wild-type strains. However, the mutants were sensitive to high-light stress, and the cpcM mutant of Synechocystis sp. strain PCC 6803 was unable to grow at moderately high light intensities. Fluorescence emission measurements showed that the ability to perform state transitions was impaired in the cpcM mutants and suggested that energy transfer from phycobiliproteins to the photosystems was also less efficient. The possible functions of asparagine N methylation of phycobiliproteins are discussed.
Expression of multiple catechol‐o‐methyltransferase (COMT) mRNA variants in human brain

Catechol‐o‐methyltransferase (COMT) is important for modulating dopamine levels, prefrontal cortex (PFC) function, and several psychiatric phenotypes. A single COMT mRNA has been described in human brain, which gives rise to membrane‐bound (MB)‐ and soluble (S)‐COMT proteins. In addition, we have recently described a novel COMT protein isoform in the human PFC, suggesting that there are more COMT gene products expressed than are currently appreciated. Therefore, we have investigated whether variant COMT mRNAs are present in human brain. We used reverse transcription‐PCR (RT‐PCR) to screen systematically for variant COMT mRNAs in human frontal cortex. Intron‐spanning primers were used for exon‐to‐exon PCR reactions; additionally, specific primers were designed to sequences in the NCBI Aceview database. The identity of amplicons was confirmed by sequencing, and their regional distributions and 3′ untranslated regions (UTRs) were characterised using RT‐PCR. We detected 7 COMT variant mRNAs, resulting from both insertions and deletions within the known COMT brain transcript. Several of the variants alter the predicted coding sequence. Three of these variants correspond to sequences within the Aceview database and could be reliably amplified, while the remaining four do not correspond to any expressed sequence tags and were amplified only once. The regional distributions of these transcripts are described. The results demonstrate multiple COMT mRNAs in human brain, revealing an additional complexity to the biology of COMT. The alternate gene products may be of significant functional importance, and differentially impacted by polymorphisms within the COMT gene. © 2007 Wiley‐Liss, Inc.
Is coffee a colonic stimulant?

BACKGROUND It is unclear if ingestion of coffee affects colonic function and if this effect is due to its caffeine content. We investigated the effects of coffee on colonic motor activity in healthy humans. METHODS We performed ambulatory colonic manometry by placing a six-sensor solid-state probe up to the mid-transverse colon in 12 healthy subjects. The following day, over a 10 h period, subjects received four stimuli: 240 ml of three drinks at 45 degrees C in random order: black Colombian coffee (150 mg caffeine), decaffeinated coffee or water and 1000 kcal meal. We analyzed the effects of each stimulant on colonic motor responses. RESULTS Caffeinated coffee, decaffeinated coffee and meal induced more activity in the colon with a greater area under the curve of pressure waves (P < 0.01) and a greater number of propagated contractions (P < 0.05) when compared with water. Caffeinated coffee, decaffeinated coffee and meal induced greater (P < 0.05) motor activity in the transverse/descending colon when compared with the rectosigmoid colon. The effects of decaffeinated coffee on colonic motility were not significantly different from those of water or caffeinated coffee and were lower (P < 0.05) than that of a meal. CONCLUSION Caffeinated coffee stimulates colonic motor activity. Its magnitude is similar to a meal, 60% stronger than water and 23% stronger than decaffeinated coffee.
Tumor Evasion of the Immune System by Converting CD4+CD25− T Cells into CD4+CD25+ T Regulatory Cells: Role of Tumor-Derived TGF-β

CD4+CD25+ T regulatory (Treg) cells were initially described for their ability to suppress autoimmune diseases in animal models. An emerging interest is the potential role of Treg cells in cancer development and progression because they have been shown to suppress antitumor immunity. In this study, CD4+CD25− T cells cultured in conditioned medium (CM) derived from tumor cells, RENCA or TRAMP-C2, possess similar characteristics as those of naturally occurring Treg cells, including expression of Foxp3, a crucial transcription factor of Treg cells, production of low levels of IL-2, high levels of IL-10 and TGF-β, and the ability to suppress CD4+CD25− T cell proliferation. Further investigation revealed a critical role of tumor-derived TGF-β in converting CD4+CD25− T cells into Treg cells because a neutralizing Ab against TGF-β, 1D11, completely abrogated the induction of Treg cells. CM from a nontumorigenic cell line, NRP-152, or irradiated tumor cells did not convert CD4+CD25− T cells to Treg cells because they produce low levels of TGF-β in CM. Finally, we observed a reduced tumor burden in animals receiving 1D11. The reduction in tumor burden correlated with a decrease in tumor-derived TGF-β. Treatment of 1D11 also reduced the conversion of CD4+ T cells into Treg cells and subsequent Treg cell-mediated suppression of antitumor immunity. In summary, we have demonstrated that tumor cells directly convert CD4+CD25− T cells to Treg cells through production of high levels of TGF-β, suggesting a possible mechanism through which tumor cells evade the immune system.
Comment on kesici and Şahin (2009): Measurement of Negative Consequences of Internet Use

In an ongoing discussion regarding use of the concept of Internet addiction, it does not seem reasonable to use the concept in studies which are conducted in nonclinical settings and describe negative situations experienced by the general population during Internet use. It may be more appropriate to discuss problematic Internet use. Dimensional rather than categorical measures would be more appropriate than Young's diagnostic criteria alone to specify whether Internet use is within a healthy range.
CloudHide: Towards Latency Hiding Techniques for Thin-client Cloud Gaming

Though there is an explosion of cloud services in recent years, cloud gaming industry is still way behind in making a strong breakthrough. Despite many benefits of cloud gaming (video or pixel streaming of rendered game scenes), the primary factor that hinders the growth is response latency, a well known issue. In this paper, we introduce a novel predictive paradigm of cloud gaming in order to mitigate latency that is inherent in cloud gaming systems. The main idea of the predictive paradigm is to pre-generate and send future outcome frames in advance to the thin-client so that the thin-client can respond immediately to any user input. The approach in this work seeks to exploit the near unlimited processing power of the cloud and ever increasing network bandwidth. The paper provides a generic and comprehensive theoretical model that shows the relationship between various parameters (network bandwidth, round-trip-time and processing time for game logic, predicting future outcomes, rendering, capturing, encoding and decoding) of predictive cloud gaming and response latency. The theocratical model design is started with an ideal server with unlimited resources for ease of understanding and then it is enhanced with resource constraints of a practically feasible non-ideal server. The model demonstrates significant amount of response latency reduction in predictive cloud gaming when compared to conventional cloud gaming. The model is analysed further to estimate the resource requirements for predictive cloud gaming. A simple game is built to demonstrate key aspects of the model and to conduct subjective evaluation of quality of experience (QoE) of the game play. The evaluations show significant gain in QoE. The resource requirements of the predictive cloud gaming gaming system grows exponentially with respect to prediction period of future frames. The paper illustrates some optimisation methods to reduce exponential growth and discusses directions for further works in this area.
Clinical experience with insulin detemir, biphasic insulin aspart and insulin aspart in people with type 2 diabetes: Results from the East India cohort of the A1chieve study

Background: The A1chieve, a multicentric (28 countries), 24-week, non-interventional study evaluated the safety and effectiveness of insulin detemir, biphasic insulin aspart and insulin aspart in people with T2DM (n = 66,726) in routine clinical care across four continents. Materials and Methods: Data was collected at baseline, at 12 weeks and at 24 weeks. This short communication presents the results for patients enrolled from East India. Results: A total of 2177 patients were enrolled in the study. Four different insulin analogue regimens were used in the study. Patients had started on or were switched to biphasic insulin aspart (n=1605), insulin detemir (n=230), insulin aspart (n=233), basal insulin plus insulin aspart (n=49) and other insulin combinations (n=54). At baseline glycaemic control was poor for both insulin naïve (mean HbA1c: 8.9%) and insulin user (mean HbA1c: 9.1%) groups. After 24 weeks of treatment, both the groups showed improvement in HbA1c (insulin naïve: -1.6%, insulin users: -1.6%). SADRs including major hypoglycaemic events or episodes did not occur in any of the study patients. Conclusion: Starting or switching to insulin analogues was associated with improvement in glycaemic control with a low rate of hypoglycaemia.
Speech-in-noise tests for multilingual hearing screening and diagnostics1.

PURPOSE New complementary multilingual speech-in-noise tests in Russian, Turkish, and Spanish for hearing self-screening purposes and follow-up hearing diagnostics are compared to the speech tests of the European project, HearCom (Hearing in the Communication Society). METHOD The tests consist of spoken numbers (Digit Triplet Test; Smits, Kapteyn, & Houtgast, 2004) or sentences (Matrix Test; e.g., Hagerman, 1982) presented in a background noise and estimate the speech reception threshold, which is the signal-to-noise ratio that yields 50% speech intelligibility. All tests were developed according to the HearCom minimum quality standards for speech intelligibility tests. This report presents a cross-language comparison of reference speech intelligibility functions for monaural headphone measurements with normal-hearing listeners. The same model function was employed to describe the speech intelligibility functions for all of the tests. RESULTS Reference speech intelligibility functions of the new versions of the Digit Triplet Test and Matrix Test show high comparability to the HearCom tests. In order to achieve the highest possible comparability across languages, language- and speaker-dependent factors in speech intelligibility should be compensated for. CONCLUSION To date, several complementary tests for screening and diagnostics have been developed in several languages. Adhering to the HearCom standards, the tests are highly comparable across languages. For the Matrix Test, equal syntax and linguistic complexity were maintained across languages due to common methodological standards.
The Suitability of Mindfulness-Based Stress Reduction for Chronic Hepatitis C

As incidence of chronic hepatitis C (CHC) in the United States increases, management of physical and psychological symptoms over the long term becomes crucial. Research has shown meditation to be a valuable tool in reducing such symptoms for various chronic illnesses. In particular, the Mindfulness-Based Stress Reduction (MBSR) program offers curriculum that has been shown to influence both physiology and perception of disease states. Although there has been no direct research to date on the effectiveness of the MBSR program for CHC, several studies have shown significant findings affecting other chronic conditions, including heart disease, fibromyalgia, and HIV. The purpose of this literature review is to examine recent research, summarize findings, and indicate appropriate inclusion of MBSR as a primary, secondary, and tertiary treatment option in conjunction with biomedical care for those diagnosed with CHC. Thusly, nurses can better inform their clients with this condition.
Automatic detection of motion direction changes in the human brain

The possibility that the visual system is able to register unattended changes is still debated in the literature. However, it is difficult to understand how a sensory system becomes aware of unexpected salient changes in the environment if attention is required for detecting them. The ability to automatically detect unusual changes in the sensory environment is an adaptive function which has been confirmed in other sensory modalities (i.e. audition). This deviance detector mechanism has proven to be based on a preattentive nonrefractory memory‐comparison process. To investigate whether such automatic change detection mechanism exists in the human visual system, we recorded event‐related potentials to sudden changes in a biologically important feature, motion direction. Unattended sinusoidal gratings varying in motion direction in the peripheral field were presented while subjects performed a central task with two levels of difficulty. We found a larger negative displacement in the electrophysiological response elicited by less frequent stimuli (deviant) at posterior scalp locations. Within the latency range of the visual evoked component N2, this differential response was elicited independently of the direction of motion and processing load. Moreover, the results showed that the negativity elicited by deviants was not related to a differential refractory state between the electrophysiological responses to frequent and infrequent directions of motion, and that it was restricted to scalp locations related to motion processing areas. The present results suggest that a change‐detection mechanism sensitive to unattended changes in motion direction may exist in the human visual system.
Cryptanalysis of the Lightweight Block Cipher Hummingbird-1

Hummingbird-1 is a lightweight cryptographic algorithm appropriated for use within resource-constrained environments, which has 256-bit key and encrypt a 16-bitdata in one operation. In this paper, a cryptanalysis ofHummingbird-1 is given which shows a shortcut attack on the internal 16-bit block length, 64-bit key block cipher. The results indicate that Hummingbird-1 may not achieve the security goal with its design choices.
Federal Funding and the Rate and Direction of Inventive Activity

Leveraging a new measure of patent citation trees (Corredoira and Banerjee, 2015), we demonstrate that research funded by the federal government is associated with more active and diverse technological trajectories. Our findings tie government funding to breakthrough inventions. The differences are especially evident at the upper percentiles of the distribution of long term patent influence and stem primarily from research conducted outside the federal government and sponsored by the DOD, HHS and NSF. Government funded patents are inputs into a broader range of technologies. Additional analyses indicate that federal programs invest in some technological areas that private corporations eschew, and federally funded university patents are in different technological classes than non-federally funded university patents. In this sense, the government may play an irreplaceable role in the rate and direction of inventive activity.
Is Protein Kinase C Activity Required for the N‐Methyl‐d‐Aspartate‐evoked Rise in Cytosolic Ca2+ in Mouse Striatal Neurons?

The present study investigates the roles of protein kinase C (PKC) and A (PKA) activities in NMDA‐mediated Ca2+ entry in primary cultures of mouse striatal neurons. Inhibitors of protein kinases, such as sphingosine, RO 31 – 8220 and staurosporine inhibited the NMDA‐ but also the KCI‐induced rise in cytosolic Ca2+. However, the PKA antagonist Rp‐adenosine‐3′,5′monophosphothioate (Rp‐cAMPS) did not alter the NMDA +d‐serine response, whereas it completely suppressed the KCI response. The NMDA +d‐serine‐evoked rise in cytosolic Ca2+, observed in the absence of external Mg2+, was potentiated by the PKC activator phorbol 12‐myristate 13‐acetate (PMA) only when submaximal effective concentrations of this agonist and co‐agonist were used. In addition, the PKC activator did not alter the NMDA +d‐serine‐evoked response in the presence of varying concentrations of Mg2+. Confirming the dependence on PKC activity, desensitization of PKC resulting from long‐term PMA treatment led to an impairment of the NMDA response, leaving the KCI‐induced response intact. We therefore propose that PKC not only potentiates but is also required for the NMDA‐evoked elevation in cytosolic Ca2+ in mouse striatal neurons.
Using a standardized‐patient examination to establish the predictive validity of the MCAT and undergraduate GPA as admissions criteria

Performance of senior medical students on an objectively scored examination of clinical competence based on standardized-patient cases was used to assess the predictive validity of the two most commonly used admission measures, the Medical College Admissions Test and the undergraduate grade point average. The students were in the classes of 1986 and 1987 at Southern Illinois University School of Medicine. The correlations of the admissions measures with clinical performances were quite weak, and none of the admissions measures consistently showed a clear advantage as a predictor of clinical performance. Correlations of the admissions measures with scores on National Board of Medical Examiners (NBME) Part I and Part II examinations were small to moderate, although somewhat larger than the correlations with clinical performances. Correlations were corrected for attenuation due to differential unreliabilities of the clinical examination results and the scores on NBME examinations, and for restriction of range due to the stringent medical school selection process. Corrected correlations were small to moderate and showed the same pattern as the uncorrected ones. The study documents that traditional admissions measures are useful for selecting students who will perform effectively in clinical as well as basic science settings.
Penetration of dentinal tubules by endodontic sealer cements in extracted teeth and in vivo.

AIM To compare the depth and consistency of penetration of three different root canal sealer cements into dentinal tubules in extracted teeth and to measure the penetration of an epoxy resin-based sealer cement in vivo. METHODOLOGY Root canals of 50 extracted human pre-molar teeth were prepared and obturated using three different sealer cements based on epoxy resin (AH26), zinc oxide eugenol (Pulp Canal Sealer EWT) and methacrylate resin (EndoREZ). Five teeth filled without sealer were used as controls. Teeth were sectioned and prepared for observation using scanning electron microscopy. A further 12 teeth with a history of successful root filling and subsequent extraction were collected and sectioned. The depth of sealer penetration into dentinal tubules was measured and the consistency and appearance of the sealer within the tubules observed. RESULTS AH26 demonstrated the deepest penetration (1337 microm), followed by EndoREZ (863 microm) and Pulp Canal Sealer EWT (71 microm). The difference in penetration between all sealer groups was found to be statistically significant (P < 0.05). The resin-based sealers appeared to penetrate tubules more consistently. In the clinical cases, all teeth demonstrated sealer penetration to varying depths (98-1490 microm). CONCLUSIONS The depth and consistency of dentinal tubule penetration of sealer cements appears to be influenced by the chemical and physical characteristics of the materials. Resin-based sealers displayed deeper and more consistent penetration. Penetration depths observed for the epoxy resin-based sealer in vivo were consistent with that found in the experimental model.
A hierarchical IP protection approach for hard IP cores

Hard IP cores are usually delivered by IP vendors for high value and performance-critical system components used in SoC designs. Although not allowing direct access to the behavioral design, hard IPs still face various IP infringements such as illegal usage and reverse engineering. This paper proposes a hierarchical IP protection approach, which combines the behavioral-level and physical-level design properties to lock each hard IP core with a key. Without the key the IP cores cannot work properly, and the design manipulation at the physical level also makes the IP cores operate incorrectly after reverse engineering, resynthesis and replacement&reroute. In addition, the key is a unique signature representing the IP vendor and the buyer, so that illegal redistribution of the IP cores can be traced. Experimental results demonstrate that the protection approach only introduces small overheads in IP cores' power consumption (<; 0.4%), area (<; 3.5%) and critical path delay (<; 3.8%). The construction of the protection circuit makes the approach secure against possible attacks.
Genomic Structures of the kW1 Loci on the Z and W Chromosomes in Ratite Birds: Structural Changes at an Early Stage of W Chromosome Differentiation

The W chromosome of ratite birds shows minimal morphological differentiation and retains homology of genetic linkage and gene order with a substantial stretch of the Z chromosome; however, the molecular structure in the differentiated region is still not well known. The kW1 sequence was isolated from the kiwi as a W-specific DNA marker for PCR-based molecular sexing of ratite birds. In ratite W chromosomes, this sequence commonly contains a ∼200-bp deletion. To characterize the very early event of avian sex chromosome differentiation, we performed molecular cytogenetic analyses of kW1 and its flanking sequences in paleognathous and neognathous birds and reptiles. Female-specific repeats were found in the kW1-flanking sequence of the cassowary (Casuarius casuarius), and the repeats have been amplified in the pericentromeric region of the W chromosomes of ratites, which may have resulted from the cessation of meiotic recombination between the Z and W chromosomes at an early stage of sex chromosome differentiation. The presence of the kW1 sequence in neognathous birds and a crocodilian species suggests that the kW1 sequence was present in the ancestral genome of Archosauria; however, it disappeared in other reptilian taxa and several lineages of neognathous birds.