Miracle-dz/UniFAR-FTUs huggingface dataset:
Large‐scale transient transfection of serum‐free suspension‐growing HEK293 EBNA1 cells: Peptone additives improve cell growth and transfection efficiency

Large‐scale transient transfection of mammalian cells is a recent and powerful technology for the fast production of milligram amounts of recombinant proteins (r‐proteins). As many r‐proteins used for therapeutic and structural studies are naturally secreted or engineered to be secreted, a cost‐effective serum‐free culture medium that allows their efficient expression and purification is required. In an attempt to design such a serum‐free medium, the effect of nine protein hydrolysates on cell proliferation, transfection efficiency, and volumetric productivity was evaluated using green fluorescent protein (GFP) and human placental secreted alkaline phosphate (SEAP) as reporter genes. The suspension growing, serum‐free adapted HEK293SF‐3F6 cell line was stably transfected with an EBNA1‐expression vector to increase protein expression when using EBV oriP bearing plasmids. Compared to our standard serum‐free medium, concomitant addition of the gelatin peptone N3 and removal of BSA slightly enhanced transfection efficiency and significantly increased volumetric productivity fourfold. Using the optimized medium formulation, transfection efficiencies between 40–60% were routinely obtained and SEAP production reached 18 mg/L−1. To date, we have successfully produced and purified over fifteen r‐proteins from 1–14‐L bioreactors using this serum‐free system. As examples, we describe the scale‐up of two secreted his‐tagged r‐proteins Tie‐2 and Neuropilin‐1 extracellular domains (ED) in bioreactors. Each protein was successfully purified to >95% purity following a single immobilized metal affinity chromatography (IMAC) step. In contrast, purification of Tie‐2 and Neuropilin‐1 produced in serum‐containing medium was much less efficient. Thus, the use of our new serum‐free EBNA1 cell line with peptone‐enriched serum‐free medium significantly improves protein expression compared to peptone‐less medium, and significantly increases their purification efficiency compared to serum‐containing medium. This eliminates labor‐intensive and expensive chromatographic steps, and allows for the simple, reliable, and extremely fast production of milligram amounts of r‐proteins within 5 days posttransfection. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 332–342, 2003.
Follow-up default in a hospital-based universal newborn hearing screening programme in a low-income country.

BACKGROUND Effective early detection of infants with permanent hearing impairment requires parental compliance with various stages of a screening protocol. However, many infants who failed initial screening tests are often not presented for follow-up evaluation, thus compromising prospects for early detection and intervention. This study set out to determine maternal and infant factors associated with loss to follow-up in a hospital-based universal hearing screening programme in a low-income country. METHODS A cross-sectional study in which babies in a tertiary maternity hospital were enrolled into a two-stage hearing screening programme with transient-evoked otoacoustic emissions followed by automated auditory brainstem response (AABR) for all transient-evoked otoacoustic emissions referrals before hospital discharge. Diagnostic evaluation was scheduled for AABR referrals on outpatient basis. Correlates of non-compliance were determined through multivariable logistic regression analyses of relevant maternal and infant factors. RESULTS Some 1330 babies participated in the first-stage screening and of 551 scheduled for AABR; 56 (10.2%) did not complete. Some 37 (84.1%) of the 44 AABR referrals did not complete the diagnostic evaluation. There were no significant differences between the profile of those who did not complete either the second-stage screening or diagnostic evaluation and those who completed across virtually all socio-demographic factors except that Christian mothers were significantly more likely not to complete the second-stage screening than diagnostic evaluation compared with their Muslim counterparts (odds ratio: 3.01; 95% confidence intervals: 1.17-7.87). The only independent predictors of non-compliance with pre-discharge screening were delivery by spontaneous vertex (odds ratio: 2.76; 95% confidence intervals: 1.47-5.19) and admission into special care baby unit (odds ratio: 5.62; 95% confidence intervals: 2.92-10.84) while no factor was predictive of non-compliance with diagnostic evaluation. CONCLUSIONS Mode of delivery or having high-risk baby influences compliance before hospital discharge while factors other than maternal or infant socio-demographic/medical profile such as unfavourable cultural beliefs and stigma may be key determinants of follow-up compliance after discharge.
Culture‐dependent and ‐independent molecular analysis of the bacterial community within uranium ore

The bacterial community structure within a uranium ore was investigated using culture‐dependent and ‐independent clone library analysis and denaturing gradient gel electrophoresis of 16S rRNA genes. The major aerobic heterotrophic bacteria were isolated and identified, and their resistance to uranium and other heavy metals was characterized. Together with near neutral pH, moderate organic carbon content, elevated U and other heavy metals (V, Ni, Mn, Cu, etc.), the ore showed high microbial counts and phylotype richness. The bacterial community mainly consisted of uncultured Proteobacteria, with the predominance of γ ‐ over β ‐ and α ‐subdivisions, along with Actinobacteria and Firmicutes. A phylogenetic study revealed that nearly one‐third of the community was affiliated to as yet uncultured and unidentified bacteria having a closer relationship to Pseudomonas. Lineages of Burkholderiaceae and Moraxellaceae were relatively more abundant in the total community, while genera affiliated to Xanthomonadaceae and Microbacteriaceae and Exiguobacterium were detected in the culturable fraction. More than 50% of the bacterial isolates affiliated to Stenotrophomonas, Microbacterium, Acinetobacter, Pseudomonas and Enterobacter showed resistance to uranium and other heavy metals. The study showed for the first time that uranium ore harbors major bacterial groups related to organisms having a wide range of environmentally significant functional attributes, and the most abundant members are possibly new groups/taxa. These findings provide new insights into U‐ore geomicrobiology that could be useful in biohydrometallurgy and bioremediation applications. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Disgust and imaginal exposure to memories of sexual trauma: Implications for the treatment of posttraumatic stress.

OBJECTIVE Emerging evidence identifies disgust as a common and persistent reaction following sexual victimization that is linked to posttraumatic stress disorder (PTSD). Importantly, evidence suggests that compared with fear, disgust may be less responsive to repeated exposure, which may have implications for the treatment of PTSD. The current study sought to fill a gap in the existing literature by examining reductions in sexual trauma cue-elicited disgust and anxiety upon repeated imaginal exposure. METHOD Seventy-two women with a history of sexual victimization completed a single laboratory-based session that involved repeated imaginal exposure to idiographic disgust- and fear-focused sexual trauma scripts. RESULTS Results demonstrated that although anxiety and disgust declined at similar rates across exposure trials (t = -.24, p = .81), ratings of disgust (B0 = 61.93) were elevated compared with ratings of anxiety at initiation (B0 = 51.03; t = 4.49, p < .001) of exposure even when accounting for severity of PTSD symptoms. Moreover, change in disgust significantly predicted improvement in script-elicited PTSD symptoms across the course of exposure for individuals exhibiting significant decline in anxiety (B = .006, t = 2.00, p = .048). Change in script-elicited PTSD symptoms was minimal (and was not predicted by the decline in disgust) for individuals exhibiting less change in anxiety (B = -.002, t = -0.46, p = .65). CONCLUSION These results add to an increasing literature documenting the importance of disgust in the development, maintenance, and treatment of sexual-trauma-related PTSD. (PsycINFO Database Record
Investigation of ischemia-modified albumin levels and some atherosclerosis-related serum parameters in patients with diabetic foot.

BACKGROUND/AIM To investigate serum ischemia-modified albumin (IMA), oxidized low-density lipoprotein (ox-LDL) levels, and paraoxonase 1 (PON1) activity in patients with diabetic foot. MATERIALS AND METHODS Thirty patients with diabetes mellitus (DM), 30 patients with diabetic foot (29 and 27 of these patients had type 2 DM, respectively), and 30 healthy volunteers as the control group were included in the study. The patients with diabetic foot were divided into 2 groups, as those who had or had not undergone lower extremity amputation. Serum PON1 activity, ox-LDL, and IMA levels were measured. RESULTS Serum PON1 activity was lower (P < 0.05) and ox-LDL levels were higher (P < 0.05) in the diabetic foot group than in the control and diabetes groups. Albumin-adjusted IMA values were higher (P < 0.001) in the diabetic foot group compared to the diabetes group. The postamputation levels of IMA were decreased compared to the preamputation condition (P < 0.05). CONCLUSION The low activity of PON1 and the high levels of ox-LDL and IMA may play an important role in the pathogenesis of diabetic foot. The use of these parameters in the follow-up of patients with DM may prevent the development of diabetic foot. In order to reach a definitive judgment, further studies with a larger number of subjects are necessary.
The Effect of Response Bias on the Personality Inventory for DSM–5 (PID–5)

ABSTRACT Valid self-report assessment of psychopathology relies on accurate and credible responses to test questions. There are some individuals who, in certain assessment contexts, cannot or choose not to answer in a manner typically representative of their traits or symptoms. This is referred to, most broadly, as test response bias. In this investigation, we explore the effect of response bias on the Personality Inventory for DSM–5 (PID–5; Krueger, Derringer, Markon, Watson, & Skodol, 2013), a self-report instrument designed to assess the pathological personality traits used to inform diagnosis of the personality disorders in Section III of DSM–5. A set of Minnesota Multiphasic Personality Inventory Restructured Form (MMPI–2–RF; Ben-Porath & Tellegen, 2008/2011) validity scales, which are used to assess and identify response bias, were employed to identify individuals who engaged in either noncredible overreporting (OR) or underreporting (UR), or who were deemed to be reporting or responding to the items in a “credible” manner—credible responding (CR). A total of 2,022 research participants (1,587 students, 435 psychiatric patients) completed the MMPI–2–RF and PID–5; following protocol screening, these participants were classified into OR, UR, or CR response groups based on MMPI–2–RF validity scale scores. Groups of students and patients in the OR group scored significantly higher on the PID–5 than those students and patients in the CR group, whereas those in the UR group scored significantly lower than those in the CR group. Although future research is needed to explore the effects of response bias on the PID–5, results from this investigation provide initial evidence suggesting that response bias influences scale elevations on this instrument.
Refractory pulmonary aspergillosis: compassionate trial with terbinafine

The frequency of bronchopulmonary aspergillosis is increasing due to the growing number of patients requiring steroids or other immunosuppressive therapies. Conventional treatments are ineffective in some patients and side–effects are an important issue. The aim of this work was to evaluate the effectiveness and safety of terbinafine, a new allylamine antimycotic drug, in three immunocompetent patients affected by lower respiratory tract aspergillosis [one chronic empyema due to Aspergillus fumigatus (AF) and two chronic necrotising aspergillosis] not responsive to the usual antimycotic therapies. In in vitro and animal model systems, terbinafine is as active as amphotericin B and itraconazole. Patients received terbinafine at doses ranging from 5 to 15 mg/kg per day, according to clinical status, for 3–5 months, depending on the clinical course of the disease and compliance. In patient 1 a negative anti–AF precipitin was obtained together with eradication of AF from the pleural cavity, which allowed a successful intrathoracic myo–omento–mammoplasty. In patients 2 and 3, AF was eradicated, anti–AF immunoprecipitins decreased, and clinical and radiological findings significantly improved. On the basis of the effectiveness of terbinafine demonstrated in this preliminary work, large studies to evaluate the use of terbinafine in bronchopulmonary aspergillosis are warranted. Moreover, the drug is not associated with resistance or significant side–effects.
Temporal structure in the light response of relay cells in the dorsal lateral geniculate nucleus of the cat.

1. The spike interval pattern during the light responses of 155 on‐ and 81 off‐centre cells of the dorsal lateral geniculate nucleus (LGN) was studied in anaesthetized and paralysed cats by the use of a novel analysis. Temporally localized interval distributions were computed from a 100 ms time window, which was shifted along the time axis in 10 ms steps, resulting in a 90% overlap between two adjacent windows. For each step the interval distribution was computed inside the time window with 1 ms resolution, and plotted as a greyscale‐coded pixel line orthogonal to the time axis. For visual stimulation, light or dark spots of different size and contrast were presented with different background illumination levels. 2. Two characteristic interval patterns were observed during the sustained response component of the cells. Mainly on‐cells (77%) responded with multimodal interval distributions, resulting in elongated ‘bands’ in the 2‐dimensional time window plots. In similar situations, the interval distributions for most (71%) off‐cells were rather wide and featureless. In those cases where interval bands (i.e. multimodal interval distributions) were observed for off‐cells (14%), they were always much wider than for the on‐cells. This difference between the on‐ and off‐cell population was independent of the background illumination and the contrast of the stimulus. Y on‐cells also tended to produce wider interval bands than X on‐cells. 3. For most stimulation situations the first interval band was centred around 6‐9 ms, which has been called the fundamental interval; higher order bands are multiples thereof. The fundamental interval shifted towards larger sizes with decreasing stimulus contrast. Increasing stimulus size, on the other hand, resulted in a redistribution of the intervals into higher order bands, while at the same time the location of the fundamental interval remained largely unaffected. This was interpreted as an effect of the increasing surround inhibition at the geniculate level, by which individual retinal EPSPs were cancelled. A changing level of adaptation can result in a mixed shift/redistribution effect because of the changing stimulus contrast and changing level of tonic inhibition. 4. The occurrence of interval bands is not directly related to the shape of the autocorrelation function, which can be flat, weakly oscillatory or strongly oscillatory, regardless of the interval band pattern. 5. A simple computer model was devised to account for the observed cell behaviour. The model is highly robust against parameter variations. (ABSTRACT TRUNCATED AT 400 WORDS)
Multivalent Antiviral XTEN–Peptide Conjugates with Long in Vivo Half-Life and Enhanced Solubility

XTENs are unstructured, nonrepetitive protein polymers designed to prolong the in vivo half-life of pharmaceuticals by introducing a bulking effect similar to that of poly(ethylene glycol). While XTEN can be expressed as a recombinant fusion protein with bioactive proteins and peptides, therapeutic molecules of interest can also be chemically conjugated to XTEN. Such an approach permits precise control over the positioning, spacing, and valency of bioactive moieties along the length of XTEN. We have demonstrated the attachment of T-20, an anti-retroviral peptide indicated for the treatment of HIV-1 patients with multidrug resistance, to XTEN. By reacting maleimide-functionalized T-20 with cysteine-containing XTENs and varying the number and positioning of cysteines in the XTENs, a library of different peptide–polymer combinations were produced. The T-20-XTEN conjugates were tested using an in vitro antiviral assay and were found to be effective in inhibiting HIV-1 entry and preventing cell death, with the copy number and spacing of the T-20 peptides influencing antiviral activity. The peptide–XTEN conjugates were also discovered to have enhanced solubilities in comparison with the native T-20 peptide. The pharmacokinetic profile of the most active T-20-XTEN conjugate was measured in rats, and it was found to exhibit an elimination half-life of 55.7 ± 17.7 h, almost 20 times longer than the reported half-life for T-20 dosed in rats. As the conjugation of T-20 to XTEN greatly improved the in vivo half-life and solubility of the peptide, the XTEN platform has been demonstrated to be a versatile tool for improving the properties of drugs and enabling the development of a class of next-generation therapeutics.
Synthetic melanin suppresses production of proinflammatory cytokines.

An overproduction of proinflammatory cytokines mediates the damaging sequelae of inflammation in pathologic conditions such as rheumatoid arthritis, graft-vs-host reaction, cachexia, and sepsis syndrome. We examined the cytokine regulatory activity of synthetic melanin, exemplified by biosynthetic l-glycine-l-tyrosine-based polymer (ME-1) and chemosynthetic dihydroxyphenylalanine-based polymer (MC-1). At nontoxic concentrations, both compounds effectively (>/=60%) and reversibly suppressed the production of tumor necrosis factor (TNF), even when applied after stimulation of human peripheral blood monocytes with lipopolysaccharide (LPS). The inhibitory activity of melanin was selective with regard to cytokine response but not inducer- or cell-type-specific. In addition to TNF, melanin inhibited production of interleukin (IL)-1beta, IL-6, and IL-10 but not granulocyte-macrophage colony-stimulating factor by the LPS-stimulated monocytes. Melanin was equally effective in inhibiting production of TNF by monocytes stimulated with the purified protein derivative of Mycobacterium tuberculosis and production of IL-6 by IL-1alpha-stimulated human fibroblasts and endothelial cells. Northern blot analysis, mRNA stability determination, immunoprecipitation studies on metabolically labeled intracellular TNF, and pulse chase experiments revealed that melanin reduced efficiency of mRNA translation. The finding that melanin arrests ongoing cytokine synthesis suggests that this compound may be useful as an adjunct therapy for conditions showing involvement of proinflammatory cytokines.
Covert Human Immunodeficiency Virus Replication in Dendritic Cells and in DC-SIGN-Expressing Cells Promotes Long-Term Transmission to Lymphocytes

ABSTRACT HIV-1 virions are efficiently captured by monocyte-derived immature dendritic cells (iDCs), as well as by cell lines expressing the lectin DC-SIGN. Viral infectivity can be retained for several days, and even enhanced, before transmission to CD4+ lymphocytes. The role of DC-SIGN in viral retention and enhancement of infection is not fully understood and varies according to the cell line expressing the lectin. We studied here the mechanisms underlying this process. We focused our study on X4-tropic human immunodeficiency virus (HIV) strains, since they were widely believed not to replicate in iDCs. However, we first show that X4 HIV replicates covertly and slowly in iDCs. This is also the case in Raji-DC-SIGN cells, which are classically used to study HIV transmission. We used either single-cycle or replicative HIV and measured viral RT and replication to further demonstrate that transfer of incoming virions from iDCs or DC-SIGN+ cells occurs only on the short-term (i.e., a few hours after viral exposure). There is no long-term storage of original HIV particles in these cells. A few days after viral exposure, replicative viruses, and not single-cycle virions, are transmitted to CD4+ cells. The cell-type-dependent activity of DC-SIGN reflects the ability of HIV to replicate covertly in some cells, and not in others.
Forming Design Teams to Develop Healthcare Information Systems

Abstract. Healthcare information systems are assuming an increasingly critical role in providing quality patient care in an effective and efficient manner. However, the success of these systems in achieving these goals remains a lingering concern. Consequently, investigating and devising strategies to enhance the likelihood of success of a healthcare information system continues to draw research interest. One strategy recommended by both researchers and practitioners alike is the participation of the target users in the design and development of the information system. However, practical considerations mandate representative, rather than universal, participation of users. Unfortunately, the information systems literature offers few guidelines for selecting user representatives to serve on a design team. This lack of guidelines easily results in system designers talking with the wrong users or managers assigning the wrong users to the design team. On the basis of the theoretical paradigms underlying the user participation and design team concepts, the authors examined and derived user characteristics that are considered the most critical criteria for selecting user members of a design team. They then report on a field survey they conducted to validate the derived criteria in healthcare information systems context. The authors conclude that the system-related functional expertise should be the primary criterion employed to select healthcare personnel to participate in system design and development. Other criteria, such as users' communication skills, computing backgrounds, and personality traits, should be given secondary considerations. Ignoring these guidelines can render user participation superfluous, resulting in system failures.