Miracle-dz/UniFAR-FTUs huggingface dataset:
Insights on the structural perturbations in human MTHFR Ala222Val mutant by protein modeling and molecular dynamics

Methylenetetrahydrofolate reductase (MTHFR) protein catalyzes the only biochemical reaction which produces methyltetrahydrofolate, the active form of folic acid essential for several molecular functions. The Ala222Val polymorphism of human MTHFR encodes a thermolabile protein associated with increased risk of neural tube defects and cardiovascular disease. Experimental studies have shown that the mutation does not affect the kinetic properties of MTHFR, but inactivates the protein by increasing flavin adenine dinucleotide (FAD) loss. The lack of completely solved crystal structure of MTHFR is an impediment in understanding the structural perturbations caused by the Ala222Val mutation; computational modeling provides a suitable alternative. The three-dimensional structure of human MTHFR protein was obtained through homology modeling, by taking the MTHFR structures from Escherichia coli and Thermus thermophilus as templates. Subsequently, the modeled structure was docked with FAD using Glide, which revealed a very good binding affinity, authenticated by a Glide XP score of −10.3983 (kcal mol−1). The MTHFR was mutated by changing Alanine 222 to Valine. The wild-type MTHFR-FAD complex and the Ala222Val mutant MTHFR-FAD complex were subjected to molecular dynamics simulation over 50 ns period. The average difference in backbone root mean square deviation (RMSD) between wild and mutant variant was found to be ~. 11 Å. The greater degree of fluctuations in the mutant protein translates to increased conformational stability as a result of mutation. The FAD-binding ability of the mutant MTHFR was also found to be significantly lowered as a result of decreased protein grip caused by increased conformational flexibility. The study provides insights into the Ala222Val mutation of human MTHFR that induces major conformational changes in the tertiary structure, causing a significant reduction in the FAD-binding affinity.
Lower and upper stem–single-stranded RNA junctions together determine the Drosha cleavage site

Significance MicroRNA genes are transcribed as long primary microRNAs (pri-miRNAs) and then processed by the Drosha–DGCR8 (DiGeorge syndrome critical region gene 8) complex into ∼60-nt pre-miRNAs, which is the key step of miRNA biogenesis. How exactly the Drosha–DGCR8 complex recognizes pri-miRNAs and selects the processing site is not well understood. Here we developed a unique approach to examining the details of how this complex chooses the processing site in human cells. Our study yields new knowledge of how the Drosha–DGCR8 complex determines its processing sites and also provides an explanation for how 5′ isomiRs are generated in some miRNAs, which is another interesting but not clearly understood phenomenon in miRNA biogenesis. Microprocessor [Drosha–DGCR8 (DiGeorge syndrome critical region gene 8) complex] processing of primary microRNA (pri-miRNA) is the critical first step in miRNA biogenesis, but how the Drosha cleavage site is determined has been unclear. Previous models proposed that the Drosha–DGCR8 complex measures either ∼22 nt from the upper stem–single-stranded RNA (ssRNA, terminal loop) junction or ∼11 nt from the lower stem–ssRNA junction to determine the cleavage site. Here, using miRNA-offset RNAs to determine the Drosha cleavage site, we show that the Microprocessor measures the distances from both the lower and upper stem–ssRNA junctions to determine the cleavage site in human cells, and optimal distances from both structures are critical to the precision of Drosha processing. If the distances are not optimal, Drosha tends to cleave at multiple sites, which can, in turn, generate multiple 5′ isomiRs. Thus, our results also reveal a mechanism of 5′ isomiR generation.
Stability-Mediated Epistasis Restricts Accessible Mutational Pathways in the Functional Evolution of Avian Hemoglobin

If the fitness effects of amino acid mutations are conditional on genetic background, then mutations can have different effects depending on the sequential order in which they occur during evolutionary transitions in protein function. A key question concerns the fraction of possible mutational pathways connecting alternative functional states that involve transient reductions in fitness. Here we examine the functional effects of multiple amino acid substitutions that contributed to an evolutionary transition in the oxygenation properties of avian hemoglobin (Hb). The set of causative changes included mutations at intradimer interfaces of the Hb tetramer. Replacements at such sites may be especially likely to have epistatic effects on Hb function since residues at intersubunit interfaces are enmeshed in networks of salt bridges and hydrogen bonds between like and unlike subunits; mutational reconfigurations of these atomic contacts can affect allosteric transitions in quaternary structure and the propensity for tetramer–dimer dissociation. We used ancestral protein resurrection in conjunction with a combinatorial protein engineering approach to synthesize genotypes representing the complete set of mutational intermediates in all possible forward pathways that connect functionally distinct ancestral and descendent genotypes. The experiments revealed that 1/2 of all possible forward pathways included mutational intermediates with aberrant functional properties because particular combinations of mutations promoted tetramer–dimer dissociation. The subset of mutational pathways with unstable intermediates may be selectively inaccessible, representing evolutionary roads not taken. The experimental results also demonstrate how epistasis for particular functional properties of proteins may be mediated indirectly by mutational effects on quaternary structural stability.
Complete remission in advanced blastic NK‐cell lymphoma/leukemia in elderly patients using the hyper‐CVAD regimen

Although its cell of origin is still controversial, the blastic NK‐cell leukemia/lymphoma clearly represents a distinct type of hematopoietic neoplasm that is particularly clinically aggressive when it occurs in elderly patients as a disseminated, multi‐organ disease. Consistently effective treatments have not been developed for this malignancy. The present report describes two elderly patients with widespread blastic NK‐cell leukemia/lymphoma involving the skin, bone marrow, peripheral blood, lymph nodes, and viscera. In both cases the malignant cells were CD56+, CD2+, and terminal deoxynucleotidyl transferase (TdT) positive with no detectable T‐cell receptor (TCR) γ chain gene rearrangement. The cells also exhibited a low CD45 expression and strong CD99 (mic‐2) expression, as seen in immature lymphoid malignancies. The above findings support the precursor NK‐cell, rather than mature NK‐ or non‐NK‐cell, origin of the malignant cells. It is noteworthy that the two patients achieved complete responses to treatment with hyper‐CVAD (fractionated cyclophosphamide, vincristine, doxorubicin, and dexamethasone) alternating with high‐dose methotrexate/cytarabine, a regimen currently utilized in acute lymphoblastic leukemia and high‐grade lymphoma. The complete remission (CR) was sustained for 24 months in one patient who received four cycles (eight courses) of the treatment. It lasted 9 months in the second patient, who received only two cycles (four courses). If similar results are obtained with future patients, a randomized study comparing the hyper‐CVAD regimen to other therapeutic strategies may be warranted. Am. J. Hematol. 74:46–51, 2003. © 2003 Wiley‐Liss, Inc.
Bone morphogenetic protein 4 and retinoic acid trigger bovine VASA homolog expression in differentiating bovine induced pluripotent stem cells

Primordial germ cells (PGCs) are the earliest identifiable and completely committed progenitors of female and male gametes. They are obvious targets for genome editing because they assure the transmission of desirable or introduced traits to future generations. PGCs are established at the earliest stages of embryo development and are difficult to propagate in vitro—two characteristics that pose a problem for their practical application. One alternative method to enrich for PGCs in vitro is to differentiate them from pluripotent stem cells derived from adult tissues. Here, we establish a reporter system for germ cell identification in bovine pluripotent stem cells based on green fluorescent protein expression driven by the minimal essential promoter of the bovine Vasa homolog (BVH) gene, whose regulatory elements were identified by orthologous modelling of regulatory units. We then evaluated the potential of bovine induced pluripotent stem cell (biPSC) lines carrying the reporter construct to differentiate toward the germ cell lineage. Our results showed that biPSCs undergo differentiation as embryoid bodies, and a fraction of the differentiating cells expressed BVH. The rate of differentiation towards BVH‐positive cells increased up to tenfold in the presence of bone morphogenetic protein 4 or retinoic acid. Finally, we determined that the expression of key PGC genes, such as BVH or SOX2, can be modified by pre‐differentiation cell culture conditions, although this increase is not necessarily mirrored by an increase in the rate of differentiation. Mol. Reprod. Dev. 83: 149–161, 2016. © 2015 Wiley Periodicals, Inc.
Inducible Hyaluronan Production Reveals Differential Effects on Prostate Tumor Cell Growth and Tumor Angiogenesis*

Prostate cancer progression can be predicted in human tumor biopsies by abundant hyaluronan (HA) and its processing enzyme, the hyaluronidase HYAL1. Accumulation of HA is dictated by the balance between expression levels of HA synthases, the enzymes that produce HA polymers, and hyaluronidases, which process polymers to oligosaccharides. Aggressive prostate tumor cells express 20-fold higher levels of the hyaluronan synthase HAS3, but the mechanistic relevance of this correlation has not been determined. We stably overexpressed HAS3 in prostate tumor cells. Adhesion to extracellular matrix and cellular growth kinetics in vitro were significantly reduced. Slow growth in culture was restored either by exogenous addition of hyaluronidase or by stable HYAL1 coexpression. Coexpression did not improve comparably slow growth in mice, however, suggesting that excess hyaluronan production by HAS3 may alter the balance required for induced tumor growth. To address this, we used a tetracycline-inducible HAS3 expression system in which hyaluronan production could be experimentally controlled. Adjusting temporal parameters of hyaluronan production directly affected growth rate of the cells. Relief from growth suppression in vitro but not in vivo by enzymatic removal of HA effectively uncoupled the respective roles of hyaluronan in growth and angiogenesis, suggesting that growth mediation is less critical to establishment of the tumor than early vascular development. Collectively results also imply that HA processing by elevated HYAL1 expression in invasive prostate cancer is a requirement for progression.
Beliefs about Supporting Mothers to Exclusively Breastfeed for 6 Months

Background: Exclusive breastfeeding rates remain low in Kenya and determinants influencing mothers’ practice are documented. Little is known about factors underlying health professionals’ intention to support mothers to continue exclusive breastfeeding. Effective behavior modification requires designing interventions at multiple levels of influence, informed by theory-based research to identify relevant determinants. Objectives: To identify salient beliefs held by health professionals about support of mothers to exclusively breastfeed for 6 months and to explore definitions of the term support. Methods: This qualitative study was conducted in 6 public health facilities in Nairobi, Kenya. We used open-ended questions based on the reasoned action approach to elicit salient consequences, referents, and circumstances perceived by 15 health professionals about support for mothers to exclusively breastfeed for 6 months. Results: The most frequently mentioned consequences were healthier babies (87%) and reduced childhood ailments (67%). The main disadvantage was human immunodeficiency virus transmission through breast milk (33%). Colleagues (80%) and managers (67%) were perceived as approving referents, whereas some mothers/couples (40%) and the breast milk substitute industry (20%) were perceived as disapproving. Facilitating circumstances included lighter workload, better training, and more time. Definitions of support were varied and included giving information and demonstrating positioning and attachment techniques. Conclusions: Overall, health professionals perceived positive consequences toward supporting exclusive breastfeeding continuation and identified a number of approving referents. However, they reported challenging circumstances in the work environment, which managers need to address to help health professionals provide the support needed by Kenyan mothers to continue exclusive breastfeeding.
Considering hyperglycemia and thrombolysis in the Stroke Hyperglycemia Insulin Network Effort (SHINE) trial

Hyperglycemia is associated with enhanced cortical toxicity and larger infarct volumes following focal cerebral ischemia. Initial blood glucose in acute ischemic stroke patients may also contribute to a differential response to thrombolysis (i.e., administration of tissue plasminogen activator (t‐PA)) and affect risk of symptomatic intracerebral hemorrhage (sICH). The Stroke Hyperglycemia Insulin Network Effort (SHINE) study is a phase III single‐blinded, randomized control trial comparing an intensive level of glucose control with standard of care glucose control in hyperglycemic stroke patients. In stratifying randomization by treatment with intravenous t‐PA, the SHINE trial offers a unique opportunity to evaluate an association between euglycemic control and outcomes from stroke thrombolysis in a prospective, comparative study. We hypothesize that normalization of blood glucose in the acute stroke setting may reduce risk of thrombolysis‐induced sICH. With enrollment recently underway, the stratified results from the SHINE trial could substantially influence future treatment decisions for hyperglycemic stroke patients.
Dissimilarity-based action recognition with the pair hidden Markov support vector machine

Human action recognition in video is highly challenging due to the substantial variations in motion performance, recording settings and inter-personal differences. Most current research focuses on the extraction of effective features and the design of suitable classifiers. Conversely, in this paper we tackle this problem by a dissimilarity-based approach where classification is performed in terms of minimum distance from templates. To measure the dissimilarity between any two action instances, we propose leveraging the Pair Hidden Markov Support Vector Machine (PHMM-SSVM) that was recently proposed for tasks of video alignment. The main advantages of PHMM-SSVM are its ability to learn optimal alignment models from training sets of manually-aligned action pairs and provide alignment scores that can be used for action classication. The experimental results over two popular action datasets show that the proposed approach has been capable of achieving an accuracy higher than many existing methods and comparable to a state-of-the-art algorithm.
An enhancer within the divergent promoter of Epstein-Barr virus responds synergistically to the R and Z transactivators

The EA-R and NotI repeat genes of Epstein-Barr virus (EBV) are oriented head to head and separated by a 1,000-base-pair (bp) divergent promoter region. We have identified functional domains within this divergent promoter which are important for regulation of the rightward EA-R gene. Both the R transactivator (Rta) and the Z transactivator (Zta) increase the abundance of correctly initiated EA-R transcripts. A 258-bp fragment (-114 to -372 from the EA-R cap site) contained the primary Rta and Zta response elements and was capable of transferring Rta and Zta activity to a heterologous promoter in an orientation- and position-independent manner. Rta activated this 258-bp enhancer region in both EBV-positive and EBV-negative cells. However, Zta activity appeared to be dependent on another EBV gene product, since Zta activated the enhancer efficiently (500- to 2,000-fold) in EBV-positive cells but had little or no activity in EBV-negative cells. The combination of Rta and Zta produced a striking synergistic effect on the enhancer in the absence of any additional EBV components, suggesting that the interaction between Zta and Rta accounts for the Zta response observed in EBV-positive cells. An Rta response element was mapped to a domain located 60 bp away from a Zta-binding site within the enhancer. Although Rta activated the enhancer and other early promoters without additional EBV- or B-cell-specific factors, it did not activate the lytic cycle of EBV, in contrast to Zta. Immunofluorescence patterns of Rta and Zta with antipeptide antisera indicated that they have overlapping but different subcellular localizations. Both transactivators were found in the nucleus, but Rta was also found in the cytoplasm.
Human tumor necrosis factor a gene regulation by virus and lipopolysaccharide

We have identified a region of the human tumor necrosis factor a (TNF-a) gene promoter that is necessary for maximal constitutive, virus-induced, and lipopolysaccharide (LPS)-induced transcription. This region contains three sites that match an NF-KB binding-site consensus sequence. We show that these three sites specifically bind NF-icB in vitro, yet each of these sites can be deleted from the TNF-a promoter with little effect on the induction of the gene by virus or LPS. Moreover, when multimers of these three sites are placed upstream from a truncated TNF-a promoter, or a heterologous promoter, an increase in the basal level of transcription is observed that is influenced by sequence context and cell type. However, these multimers are not sufficient for virus or LPS induction of either promoter. Thus, unlike other virus- and LPS-inducible promoters that contain NF-#cB binding sites, these sites from the TNF-ai promoter are neither required nor sufficient for virus or LPS induction. Comparison of the sequence requirements of virus induction of the human TNF-a gene in mouse L929 and P388D1 cells reveals significant differences, indicating that the sequence requirements for virus induction of the gene are cell 'type-specific. However, the sequences required for virus and LPS induction of the gene in a single cell type, P388D1, overlap. The
An Inline-Type Microwave Power Sensor Based on MEMS Technology

The theory, design, fabrication and measurements of a novel structure for measuring power of microwave signals are presented. The novelty of this sensor is that it measures the microwave power coupled from the CPW line by the MEMS membrane. In this method the signal is available during the power detection. The fabrication of the power sensor is fully compatible with the GaAs MMIC process. The design, fabrication and experiment results of this sensor are given. In order to reduce the reflection losses of the sensor, an improvement of the sensor with an inductively tuned structure is presented and simulated.
Complement activation products in liquid stored plasma and C3a kinetics after transfusion of autologous plasma

Background and Objectives Keeping a small stock of liquid plasma readily available for transfusion is common practise in Sweden. We report data on complement activation markers in plasma components during storage in the liquid state and the kinetics of C3a‐desArg after transfusion of autologous plasma with high content of C3a‐desArg.
Effects of acetazolamide on ventilatory, cerebrovascular, and pulmonary vascular responses to hypoxia.

RATIONALE Acute mountain sickness (AMS) may affect individuals who (rapidly) ascend to altitudes higher than 2,000-3,000 m. A more serious consequence of rapid ascent may be high-altitude pulmonary edema, a hydrostatic edema associated with increased pulmonary capillary pressures. Acetazolamide is effective against AMS, possibly by increasing ventilation and cerebral blood flow (CBF). In animals, it inhibits hypoxic pulmonary vasoconstriction. OBJECTIVES We examined the influence of acetazolamide on the response to hypoxia of ventilation, CBF, and pulmonary vascular resistance (PVR). METHODS In this double-blind, placebo-controlled, randomized study, nine subjects ingested 250 mg acetazolamide every 8 h for 3 d. On the fourth test day, we measured the responses of ventilation, PVR, and CBF to acute isocapnic hypoxia (20 min) and sustained poikilocapnic hypoxia (4 h). Ventilation was measured with pneumotachography. Hypoxia was achieved with dynamic end-tidal forcing. The maximum pressure difference across the tricuspid valve (DeltaPmax, a good index of PVR) was measured with Doppler echocardiography. CBF was measured by transcranial Doppler ultrasound. RESULTS In normoxia, acetazolamide increased ventilation and reduced DeltaPmax, but did not influence CBF. The ventilatory and CBF responses to acute isocapnic hypoxia were unaltered, but the rise in DeltaPmax was reduced by 57%. The increase in DeltaPmax by sustained poikilocapnic hypoxia observed after placebo was reduced by 34% after acetazolamide, the ventilatory response was increased, but the CBF response remained unaltered. CONCLUSIONS Acetazolamide has complex effects on ventilation, PVR, and CBF that converge to optimize brain oxygenation and may be a valuable means to prevent/treat high-altitude pulmonary edema.
EFFECT OF STRESS ON THE PERCENT BODY WEIGHT CHANGE AND MRNA EXPRESSION OF IGF-1, SURVIVINE AND HSP-70 GENE IN THE HIERARCHIAL FOLLICLES OF JAPANESE QUAIL

The present study was carried out to explore the effect of stress on body weight and the mRNA expression of IGF-1, Survivine and HSP-70 gene in the hierarchial follicles of Japanese quail. A total 24 birds (10 weeks) were taken and stress was induced by immobilization daily for 2hrs (between 9.00 - 11.00 AM) throughout the study (10 days). Four birds were sacrificed on 1, 2, 4, 6, 8 and 10 days of the treatment. Hierarchial follicles (F1, F2 & F3) were aseptically collected to quantify the expression of IGF-1, Survivine and HSP-70 gene using real-time PCR technique. The percent body weight reduction increased and reached highest (21.30%) on 10 th day. The fold expression of IGF-1 gene was significantly ((P=0.05) down regulated in advance to the time of experiment. However, the fold expression of survivine gene was significantly (P=0.05) up regulated and the intensity was highest (17 fold) in F-3 follicle on 4 th day of experiment. No significant change in the mRNA expression of HSP-70