Miracle-dz/UniFAR-FTUs huggingface dataset:
CHO cell line specific prediction and control of recombinant monoclonal antibody N‐glycosylation

Here we demonstrate that it is possible to predict and control N‐glycan processing of a secreted recombinant monoclonal antibody during manufacturing process development using a combination of statistical modelling and comparative measurement of cell surface glycans using fluorescent lectins. Using design of experiments—response surface modelling (DoE‐RSM) methodology to adjust the relative media concentrations of known metabolic effectors of galactosylation (manganese, galactose, and uridine) we have shown that β1,4‐galactosylation of the same recombinant IgG4 monoclonal antibody produced by different CHO cell lines can be precisely controlled in a cell line specific manner. For two cell lines, monoclonal antibody galactosylation could be increased by over 100% compared to control, non‐supplemented cultures without a reduction in product titre and with minimal effect on cell growth. Analysis of galactosylation effector interactions by DoE‐RSM indicated that Mn2+ alone was necessary but not sufficient to improve galactosylation, and that synergistic combinations of Gal and Urd were necessary to maximize galactosylation, whilst minimizing the deleterious effect of Urd on cell growth. To facilitate rapid cell culture process development we also tested the hypothesis that substrate‐level control of cellular galactosylation would similarly affect both cell surface and secreted monoclonal antibody glycans, enabling facile indirect prediction of product glycan processing. To support this hypothesis, comparative quantitation of CHO cell surface β1,4‐galactosylation by flow cytometry using fluorescent derivatives of RCA and ConA lectins revealed that substrate‐controlled variation in monoclonal antibody galactosylation and cell surface galactosylation were significantly correlated. Taken together, these data show that precision control of a complex, dynamic cellular process essential for the definition of protein product molecular heterogeneity and bioactivity is possible. Moreover, real‐time, or near real‐time control can be enabled by facile, rapid measurement of cell surface biomarkers of cellular biosynthetic capability. Biotechnol. Bioeng. 2013;110: 2970–2983. © 2013 Wiley Periodicals, Inc.
Two Novel Real-Time Reverse Transcriptase PCR Assays for Rapid Detection of Bacterial Contamination in Platelet Concentrates

ABSTRACT The incidence of platelet bacterial contamination is approximately 1 per 2,000 units and has been acknowledged as the most frequent infectious risk from transfusion. In preliminary studies, the sterility of platelet concentrates (PCs) was tested with an automated bacterial blood culturing system and molecular genetic assays. Two real-time reverse transcriptase PCR (RT-PCR) assays performed in a LightCycler instrument were developed and compared regarding specificity and sensitivity by the use of different templates to detect the majority of the clinically important bacterial species in platelets. Primers and probes specific for the conserved regions of the eubacterial 23S rRNA gene or the groEL gene (encoding the 60-kDa heat shock protein Hsp60) were designed. During the development of the 23S rRNA RT-PCR, problems caused by the contamination of reagents with bacterial DNA were noted. Treatment with 8-methoxypsoralen and UV irradiation reduced the level of contaminating DNA. The sensitivity of the assays was greatly influenced by the enzyme system which was used. With rTth DNA polymerase in a one-enzyme system, we detected 500 CFU of Escherichia coli or Staphylococcus epidermidis/ml. With a two-enzyme system consisting of Moloney murine leukemia virus RT and Taq DNA polymerase, we detected 16 CFU/ml. With groEL mRNA as the target of RT-PCR under optimized conditions, we detected 125 CFU of E. coli/ml, and no problems with false-positive results caused by reagent contamination or a cross-reaction with human nucleic acids were found. Furthermore, the use of mRNA as an indicator of viability was demonstrated. Here we report the application of novel real-time RT-PCR assays for the detection of bacterial contamination of PCs that are appropriate for transfusion services.
Ground plan of the insect mushroom body: Functional and evolutionary implications

In most insects with olfactory glomeruli, each side of the brain possesses a mushroom body equipped with calyces supplied by olfactory projection neurons. Kenyon cells providing dendrites to the calyces supply a pedunculus and lobes divided into subdivisions supplying outputs to other brain areas. It is with reference to these components that most functional studies are interpreted. However, mushroom body structures are diverse, adapted to different ecologies, and likely to serve various functions. In insects whose derived life styles preclude the detection of airborne odorants, there is a loss of the antennal lobes and attenuation or loss of the calyces. Such taxa retain mushroom body lobes that are as elaborate as those of mushroom bodies equipped with calyces. Antennal lobe loss and calycal regression also typify taxa with short nonfeeding adults, in which olfaction is redundant. Examples are cicadas and mayflies, the latter representing the most basal lineage of winged insects. Mushroom bodies of another basal taxon, the Odonata, possess a remnant calyx that may reflect the visual ecology of this group. That mushroom bodies persist in brains of secondarily anosmic insects suggests that they play roles in higher functions other than olfaction. Mushroom bodies are not ubiquitous: the most basal living insects, the wingless Archaeognatha, possess glomerular antennal lobes but lack mushroom bodies, suggesting that the ability to process airborne odorants preceded the acquisition of mushroom bodies. Archaeognathan brains are like those of higher malacostracans, which lack mushroom bodies but have elaborate olfactory centers laterally in the brain. J. Comp. Neurol. 513:265–291, 2009. © 2009 Wiley‐Liss, Inc.
Prognostic value of angiogenesis evaluated with high-frequency and color Doppler sonography for preoperative assessment of melanomas.

OBJECTIVE The aim of our study was to confirm the value of high-frequency and color Doppler sonography in evaluating the metastatic potential of melanomas. SUBJECTS AND METHODS Sixty-nine histologically proven melanomas in 67 patients were prospectively studied before surgical resection. A morphologic study was performed with a 20-MHz probe. The maximal thickness of tumors was measured and compared with the Breslow index. A color Doppler sonographic analysis of neovascularization was performed with a 13-MHz probe to depict intratumoral vessels. RESULTS Of the 69 melanomas, 65 were depicted on sonography. Tumor thickness ranged from 0.26 to 8.0 mm as measured by sonography and from 0.15 to 8.0 mm according to the Breslow index. Sonographic measurements correlated strongly with the Breslow index (r > 0.96). Surgical reexcision was necessary in 33 tumors with a Breslow index exceeding 1 mm, but reexcision could have been avoided in 31 of these cases had the initial surgical planning been based on high-frequency sonographic measurements. Among the 62 patients studied with color Doppler sonography, intratumoral vessels were depicted on color Doppler sonography in 21 melanomas, all of which were thicker than 2 mm. The median follow-up was 40 months. Eleven patients developed metastases, and all except one had a vascularized melanoma. In the univariate analyses, neovascularization visualized with sonography and the Breslow index were both significantly linked to the occurrence of metastases (p < 0.0001). In the multivariate Cox proportional hazards regression analysis, neovascularization was the only significant parameter. CONCLUSION This study confirms that prognostic value of angiogenesis evaluated with color Doppler sonography could be used to identify melanomas with a high metastatic potential.
Prognosis of patients with lymph node positive prostate cancer following radical prostatectomy: long-term results.

PURPOSE We determined the prognostic factors that affect recurrence and survival in patients with lymph node positive prostate cancer. MATERIALS AND METHODS Between 1972 and 1999, 1,936 patients underwent radical retropubic prostatectomy and pelvic lymph node dissection for clinically organ confined prostate cancer. A total of 235 patients (12.1%) were found to have disease metastatic to the lymph nodes (stage D1). Of the patients 69% received no adjuvant treatment. We reviewed the tumor stage (TNM), Gleason score, number and percent of involved lymph nodes (lymph node density), preoperative prostate specific antigen when available and adjuvant treatment. Overall survival and recurrence-free survival were estimated using Kaplan-Meier plots. RESULTS Followup was 1 to 24 years (median 11.4). Overall median survival was 15 years. Overall clinical recurrence-free survival at 5, 10 and 15 years was 80%, 65% and 58%, respectively. Patients who had 1 or 2 positive lymph nodes had a clinical recurrence-free survival of 70% and 73% at 10 years, respectively, vs 49% in those who had 5 or more involved lymph nodes (p = 0.0031). When stratified by lymph node density, patients with a lymph node density of 20% or greater were at higher risk for clinical recurrence compared to those with a density of less than 20% (relative risk = 2.32, p <0.0001). On stratified log rank test only prostate cancer T stage, and the number and percent of positive lymph nodes correlated with recurrence-free and overall survival. CONCLUSIONS Local tumor bulk and the number/percent of involved lymph nodes significantly affect disease progression and the survival rate. Radical prostatectomy may offer long-term survival in patients who have limited tumor bulk and nodal involvement.
Mechanism of dye binding in the protein assay using eosin dyes.

Eosin B and eosin Y have been used to estimate micro- and submicrogram quantities of proteins respectively as shown in our previous reports. In the present study we describe the mechanism of eosin binding to proteins. At pH lower than 3.0 the absorbance of unbound dye is greatly reduced. After the dye binds to protein, the absorption maximum of the dye changes from 514 to 530 +/- 5 nm. The absorbance and bathochromatic shift in absorption maximum of the protein-dye complex are proportional to the concentration of protein. The pH of the assay solution does not change due to protein. Arginine, histidine, and lysine (at both acidic and neutral pH) and tryptophan (at acidic pH) residues of a protein bind electrostatically to carboxylic and phenolic groups of the dye to produce a stable water-soluble protein-dye complex. The binding constants of eosin B with poly-L-arginine, poly-L-histidine, poly-L-lysine, and poly-L-tryptophan at pH 1.96 are 0.37, 0.32, 0.33 and 0.33 nmol/nmol of amino acid, respectively. The binding constants of eosin B and eosin Y with bovine serum albumin (BSA) at pH 1.96 are essentially the same, i.e., 0.82 nmol/nmol of reactive amino acid of BSA. The binding constant varies with solution pH so that a wide range of protein concentrations can be estimated. The reason for the higher absorbance of protein-eosin Y complex compared to that of protein-eosin B complex is discussed.
Space-Time Block Coding for Uplink Single-Carrier CDMA with Joint Detection in the Frequency Domain

Single-carrier code-division multiple access (SC-CDMA), also named cyclic-prefix CDMA in the literature, is a promising air interface for the uplink of the 4G cellular wireless communication systems. It enables the high capacity intrinsically offered by CDMA by making the equalization of the multipath channels and the mitigation of the resulting interference possible at a low complexity. This paper proposes a new air interface that combines SC-CDMA with space-time block coding (STBC) across multiple transmit antennas in order to make the link more robust. Contrary to existing air interfaces that perform the STBC at the chip level, making them only applicable to the downlink, the STBC is performed at the symbol level, making it also applicable to the uplink. In order to optimally detect the different antenna and user signals, a linear joint detector optimized according to the minimum mean square error (MMSE) criterion is designed. By exploiting the cyclic properties of the channel matrices, the complexity of the joint detector is significantly reduced. Furthermore, it is shown analytically that the inter-antenna interference is canceled out at the output of the first stage of the linear MMSE joint detector, consisting of a matched filter. By space-time coding the signal through two antennas at each transmit mobile terminal, a significant gain in signal-to-noise-ratio can be achieved. However, the spatial diversity gain of the proposed system is limited by the multiuser interference (MUI), that is increasing with the user load. Higher complexity non-linear receivers are needed to better compensate the MUI and still benefit from the spatial diversity at high user loads.
Warren Buffett Value Indicator vs. GDP Size ─ Is the Relationship Superlinear?

Warren Buffett value indicator or Buffett indicator is the ratio of financial capitalisation to GDP for a given time for a country. Buffett indicator is used as a buy or sell signal to many investors around the world. This paper attempts to determine whether the scaling relationship may exist for Buffett indicator among different groups of countries. If such scaling relationship exists, the traditional use of Buffett indicator can be refined to seek better candidate countries for investment. Our analysis indicates that superlinear scaling relationship exists for total of 34 countries during the period of 1997 to 2014. Superlinear relationship exists also for the subgroups of 12 and 13 countries, but not for the subgroup of nine countries. Implication from our findings for international investment will be discussed.
Modulation of TASK-1 (Kcnk3) and TASK-3 (Kcnk9) Potassium Channels

TASK-1 and TASK-3, members of the two-pore-domain channel family, are widely expressed leak potassium channels responsible for maintenance of cell membrane potential and input resistance. They are sites of action for a variety of modulatory agents, including volatile anesthetics and neurotransmitters/hormones, the latter acting via mechanisms that have remained elusive. To clarify these mechanisms, we generated mutant channels and found that alterations disrupting anesthetic (halothane) activation of these channels also disrupted transmitter (thyrotropin-releasing hormone, TRH) inhibition and did so to a similar degree. For both TASK-1 and TASK-3, mutations (substitutions with corresponding residues from TREK-1) in a six-residue sequence at the beginning of the cytoplasmic C terminus virtually abolished both anesthetic activation and transmitter inhibition. The only sequence motif identified with a classical signaling mechanism in this region is a potential phosphorylation site; however, mutation of this site failed to disrupt modulation. TASK-1 and TASK-3 differed insofar as a large portion of the C terminus was necessary for the full effects of halothane and TRH on TASK-3 but not on TASK-1. Finally, tandem-linked TASK-1/TASK-3 heterodimeric channels were fully modulated by anesthetic and transmitter, and introduction of the identified mutations either into the TASK-1 or the TASK-3 portion of the channel was sufficient to disrupt both effects. Thus, both anesthetic activation and transmitter inhibition of these channels require a region at the interface between the final transmembrane domain and the cytoplasmic C terminus that has not been associated previously with receptor signal transduction. Our results also indicate a close molecular relationship between these two forms of modulation, one endogenous and the other clinically applied.
Development of Functional If Channels in mMSCs after Transfection with mHCN4: Effects on Cell Morphology and Mechanical Activity in vitro

Objective: To study the functional properties of If channels and the changes in mechanical activity of mouse mesenchymal stem cells (mMSCs) transfected with mHCN4. Methods: mMSCs were purified by using CD11b-immunomagnetic microbeads and transfected with pMSCV-mHCN4-EGFP or pMSCV-EGFP. We examined the kinetic characteristics of the mHCN4 channel. The morphological changes of positively transfected mMSCs were investigated at the same time. Results: The If current recorded from the experimental group was sensitive to extracellular Cs+ (–44.5 ± 4.2 vs. –5.5 ± 1.0 pA/pF, p < 0.001). The half-maximal activation was –99.0 ± 5.8 mV. The time constant of activation was 451 ± 61 ms under –140 mV. The control cells did not show the current under the same conditions. The absolute values of half-maximal activation decreased in the presence of cAMP or cGMP in the experimental group (–78.6 ± 10.4 and –85.7 ± 8.6 vs. –99.0 ± 5.8 mV, respectively, p < 0.05). mMSCs transfected with pMSCV-mHCN4-EGFP could form spontaneous beating cells. Extracellular Cs+ decreased the beating rate significantly (196 ± 50 vs. 66 ± 23 bmp, p < 0.01). Conclusions: Functional If channels can be reconstructed in mMSCs infected with mHCN4. mMSCs modified by successful transfection with mHCN4 can differentiate so as to develop spontaneous mechanical activity.
Ad hoc network routing and security: A review

Ad hoc network is a collection of wireless mobile nodes dynamically forming a local area network without the use of any existing network infrastructure or centralized administration. One problem in the design of such network is its wireless vulnerabilities and limited physical security. This paper considers the security attributes and goals of ad hoc network, reviews the latest developments of current routing and security mechanissm including encryption, protocols, user authentication, and physical security. It also explores the new approaches trying to solve current problems and points out the future research directions. These methods will be helpful in the military and other security‐sensitive fields. Copyright © 2006 John Wiley & Sons, Ltd.
Predictors for Lower Quality of Life in the HAART Era Among HIV-Infected Men

Background: In the era of highly active antiretroviral therapy (HAART), maximizing health-related quality of life (QOL) has become a high priority of long-term management of HIV-infected individuals. Modifiable determinants of lower QOL should be identified for interventions specifically targeted to the HAART-using individuals to improve their QOL. Objective: To identify the predictors for lower QOL among HAART-using study participants in the Multicenter AIDS Cohort Study, a longitudinal study of HIV infection among homosexual and bisexual men in 4 cities. Methods: In the Multicenter AIDS Cohort Study, 636 HAART-using subjects had QOL data before HAART initiation and at least 2 consecutive QOL measurements after HAART initiation to visit 40 (April 2004). Variables of sociodemographics, individual risk behaviors, social support, biological markers, HIV-related medication use and clinical outcome indicators preceding the study outcomes, the physical health summary score and the mental health summary score derived from the standard SF-36 QOL form, were assessed as possible predictors using random-effects mixed models. Results: QOL before HAART initiation was a strong predictor of QOL subsequent to HAART initiation. Older age, lower socioeconomic status, less male sexual partners, no alcohol drinking, and more advanced HIV disease stage were significant predictors for lower physical health summary score. In addition, more outpatient visits, depression, amprenavir use, antiretroviral drug interruption, recreational drug use, and less social support were significantly associated with lower mental health summary score. Discussion: Many predictors of lower QOL are alterable risk factors that can be effectively targeted for interventions to maximize patients' QOL. With appropriate treatment and management of HIV disease and depression, clinicians can help improve the QOL of their patients. Through modification of individual risk behaviors, HIV-infected individuals can enhance their own QOL with support from clinicians and the community. In addition, active social support can also be an effective way to improve mental health of the infected persons.
Electromagnetic field in a dispersive medium filled cavity under pulse train excitation

Electromagnetic field in a cavity filled with temporary dispersive homogeneous isotropic medium is excited by a train of wideband current pulses. The solution is obtained in the time domain. Several frequency dependences of permittivity and permeability are considered. Peculiarities of choosing the pulse train parameters for cavity excitation in different cases are discussed.
Diversity and abundance of resupinate thelephoroid fungi as ectomycorrhizal symbionts in Swedish boreal forests

Resupinate thelephoroid fungi (hereafter called tomentelloid fungi) have a world‐wide distribution and comprise ≈70 basidiomycete species with inconspicuous, resupinate sporocarps. It is only recently that their ability to form ectomycorrhizas (EM) has been realized, so their distribution, abundance and significance as mycobionts in forest ecosystems is still largely unexplored. In order to provide baseline data for future ecological studies of tomentelloid fungi, we explored their presence and abundance in nine Swedish boreal forests in which the EM communities had been analysed. Phylogenetic analyses were used to compare the internal transcribed spacer of nuclear ribosomal DNA (ITS rDNA) sequence data obtained from mycobionts on single ectomycorrhizal tips with that obtained from sporocarps of identified tomentelloid fungi. Five species of Tomentella and one species of Pseudotomentella were identified as ectomycorrhizal fungi. The symbiotic nature of Tomentella bryophila, T. stuposa, T. badia and T. atramentaria is demonstrated for the first time. T. stuposa and Pseudotomentellatristis were the most commonly encountered tomentelloid fungi, with the other species, including T. sublilacina, only being recorded from single stands. Overall, tomentelloid fungi were found in five of the studies, colonizing between 1 and 8% of the mycorrhizal root tips. Two of the five sites supported several tomentelloid species. Tomentelloid fungi appear to be relatively common ectomycorrhizal symbionts with a wide distribution in Swedish coniferous forests. The results are in accordance with accumulating data that fungal species which lack conspicuous sporocarps may be of considerable importance in EM communities.