Miracle-dz/UniFAR-FTUs huggingface dataset:
Allosteric Activation of a G Protein-coupled Receptor with Cell-penetrating Receptor Mimetics*

Background: Intracellular parts of GPCRs have yet to be effectively exploited as allosteric modulators. Results: The structure and mechanism of action of a lipidated pepducin agonist is determined. Conclusion: The pepducin requires the H8 helix and TM7 tyrosine propeller to stabilize the on-state and trigger receptor-G protein signaling. Significance: This work provides critical insight into the identification of allosteric modulators to this major drug target class. G protein-coupled receptors (GPCRs) are remarkably versatile signaling systems that are activated by a large number of different agonists on the outside of the cell. However, the inside surface of the receptors that couple to G proteins has not yet been effectively modulated for activity or treatment of diseases. Pepducins are cell-penetrating lipopeptides that have enabled chemical and physical access to the intracellular face of GPCRs. The structure of a third intracellular (i3) loop agonist, pepducin, based on protease-activated receptor-1 (PAR1) was solved by NMR and found to closely resemble the i3 loop structure predicted for the intact receptor in the on-state. Mechanistic studies revealed that the pepducin directly interacts with the intracellular H8 helix region of PAR1 and allosterically activates the receptor through the adjacent (D/N)PXXYYY motif through a dimer-like mechanism. The i3 pepducin enhances PAR1/Gα subunit interactions and induces a conformational change in fluorescently labeled PAR1 in a very similar manner to that induced by thrombin. As pepducins can potentially be made to target any GPCR, these data provide insight into the identification of allosteric modulators to this major drug target class.
Co-chaperone Specificity in Gating of the Polypeptide Conducting Channel in the Membrane of the Human Endoplasmic Reticulum*

Background: The molecular chaperone immunoglobulin heavy-chain-binding protein (BiP) modulates gating of the polypeptide-conducting and calcium-permeable channel (Sec61 complex) in the membrane of the endoplasmic reticulum (ER). Results: Two co-chaperones, ERj3 and ERj6, support BiP in preventing ER calcium leakage via Sec61 complex. Conclusion: ERj3 and ERj6 facilitate Sec61 channel closing. Significance: Different co-chaperones assist BiP in Sec61 channel gating. In mammalian cells, signal peptide-dependent protein transport into the endoplasmic reticulum (ER) is mediated by a dynamic polypeptide-conducting channel, the heterotrimeric Sec61 complex. Previous work has characterized the Sec61 complex as a potential ER Ca2+ leak channel in HeLa cells and identified ER lumenal molecular chaperone immunoglobulin heavy-chain-binding protein (BiP) as limiting Ca2+ leakage via the open Sec61 channel by facilitating channel closing. This BiP activity involves binding of BiP to the ER lumenal loop 7 of Sec61α in the vicinity of tyrosine 344. Of note, the Y344H mutation destroys the BiP binding site and causes pancreatic β-cell apoptosis and diabetes in mice. Here, we systematically depleted HeLa cells of the BiP co-chaperones by siRNA-mediated gene silencing and used live cell Ca2+ imaging to monitor the effects on ER Ca2+ leakage. Depletion of either one of the ER lumenal BiP co-chaperones, ERj3 and ERj6, but not the ER membrane-resident co-chaperones (such as Sec63 protein, which assists BiP in Sec61 channel opening) led to increased Ca2+ leakage via Sec6 complex, thereby phenocopying the effect of BiP depletion. Thus, BiP facilitates Sec61 channel closure (i.e. limits ER Ca2+ leakage) via the Sec61 channel with the help of ERj3 and ERj6. Interestingly, deletion of ERj6 causes pancreatic β-cell failure and diabetes in mice and humans. We suggest that co-chaperone-controlled gating of the Sec61 channel by BiP is particularly important for cells, which are highly active in protein secretion, and that breakdown of this regulatory mechanism can cause apoptosis and disease.
The Care of Pets Within Child Abusing Families

The treatment of animals was surveyed in 53 families in which child abuse had occurred. Patterns of pet ownership, attitudes towards pets and quality of veterinary care did not differ greatly from comparable data from the general public. However, abuse of pets by a family member had taken place in 60 percent of the families. The families in which animal abuse was indicated tended to have younger pets, lower levels of veterinary care and more conflicts over care than non-abusive families in.
Cellular FLICE-like Inhibitory Protein (c-FLIP) and PS1-associated Protein (PSAP) Mediate Presenilin 1-induced γ-Secretase-dependent and -independent Apoptosis, Respectively*

Background: The PS1-induced apoptosis mechanism is not fully understood. Results: PS1-induced apoptosis depends on PSAP-Bax complex formation and γ-catalyzed turnover of c-FLIP. Conclusion: PS1 induces apoptosis through the γ-secretase-dependent PS1-c-FLIP-caspase-8-Bid cascade and γ-secretase-independent PS1-PSAP cascade, which converge on Bax to activate the mitochondrial apoptotic pathway. PS2 induced apoptosis through a different pathway. Significance: This study provides new insight into the mechanism of PS1-induced apoptosis. Presenilin 1 (PS1) has been implicated in apoptosis; however, its mechanism remains elusive. We report that PS1-induced apoptosis was associated with cellular FLICE-like inhibitory protein (c-FLIP) turnover and that γ-secretase inhibitor blocked c-FLIP turnover and also partially blocked PS1-induced apoptosis. A complete inhibition of PS1-induced apoptosis was achieved by knockdown of PS1-associated protein (PSAP), a mitochondrial proapoptotic protein that forms a complex with Bax upon induction of apoptosis, in the presence of γ-secretase inhibitor. PS1-induced apoptosis was partially inhibited by knockdown of caspase-8, Fas-associated protein with death domain (FADD), or Bid. However, knockdown of Bax or overexpression of Bcl-2 resulted in complete inhibition of PS1-induced apoptosis. These data suggest that PS1 induces apoptosis through two pathways: the γ-secretase-dependent pathway mediated by turnover of c-FLIP and the γ-secretase-independent pathway mediated by PSAP-Bax complex formation. These two pathways converge on Bax to activate mitochondria-dependent apoptosis. These findings provide new insight into the mechanisms by which PS1 is involved in apoptosis and the mechanism by which PS1 exerts its pathogenic effects. In addition, our results suggest that PS2 induces apoptosis through a pathway that is different from that of PS1.
Substrate Efflux Propensity Is the Key Determinant of Ca2+-independent Phospholipase A-β (iPLAβ)-mediated Glycerophospholipid Hydrolysis*

Background: Ca2+-independent phospholipase A-β (iPLAβ) has been repeatedly implicated as a homeostatic enzyme. Results: Activity of iPLAβ correlates inversely with the hydrophobicity of the phospholipid substrate. Conclusion: Efflux of the phospholipid substrate from a membrane mainly determines the activity of iPLAβ. Significance: Results support the role of iPLAβ as a homeostatic enzyme that responds to increased phospholipid efflux proposed to occur at particular “critical” compositions. The A-type phospholipases (PLAs) are key players in glycerophospholipid (GPL) homeostasis and in mammalian cells; Ca2+-independent PLA-β (iPLAβ) in particular has been implicated in this essential process. However, the regulation of this enzyme, which is necessary to avoid futile competition between synthesis and degradation, is not understood. Recently, we provided evidence that the efflux of the substrate molecules from the bilayer is the rate-limiting step in the hydrolysis of GPLs by some secretory (nonhomeostatic) PLAs. To study whether this is the case with iPLAβ as well, a mass spectrometric assay was employed to determine the rate of hydrolysis of multiple saturated and unsaturated GPL species in parallel using micelles or vesicle bilayers as the macrosubstrate. With micelles, the hydrolysis decreased with increasing acyl chain length independent of unsaturation, and modest discrimination between acyl positional isomers was observed, presumably due to the differences in the structure of the sn-1 and sn-2 acyl-binding sites of the protein. In striking contrast, no significant discrimination between positional isomers was observed with bilayers, and the rate of hydrolysis decreased with the acyl chain length logarithmically and far more than with micelles. These data provide compelling evidence that efflux of the substrate molecule from the bilayer, which also decreases monotonously with acyl chain length, is the rate-determining step in iPLAβ-mediated hydrolysis of GPLs in membranes. This finding is intriguing as it may help to understand how homeostatic PLAs are regulated and how degradation and biosynthesis are coordinated.
Improving women's sexual health: a quantitative evaluation of an educational intervention for healthcare professionals

Forty-three per cent of women in the USA report some type of sexual complaint and these complaints have been shown to negatively impact quality of life and overall well-being. With proper training and experience, healthcare professionals are in a unique position to help their patients improve their sexual health. The present study was designed to increase knowledge about female sexual dysfunction by offering a continuing education workshop combining didactic and experiential learning. Healthcare professionals representing the specialties of obstetrics, gynaecology, primary care, psychiatry and psychology attended the conference. Participants completed a pre- and post-test questionnaire assessing levels of comfort, competence, attitudes toward female sexual health and readiness for change. Using the pre- and post-test questionnaire, participants reported a significant increase in awareness about the importance of discussing issues of sexual health with their patients. Participants also reported motivation (or intent) to ask their patients about their sexual health. Providing information about female sexual dysfunction and its impact on patients' quality of life, effective treatments and referral resources as well as giving healthcare professionals an opportunity to practise asking about sexual health with facilitated feedback may significantly improve their motivation to respond to female sexual complaints.
Structural Basis for Penetration of the Glycan Shield of Hepatitis C Virus E2 Glycoprotein by a Broadly Neutralizing Human Antibody*

Background: HCV uses glycan shielding to mask epitopes recognized by neutralizing antibodies. Results: The structure of a human antibody bound to an HCV E2 epitope revealed how it penetrates a shield created by glycosylation shifting. Conclusion: Antibody binding induces an epitope conformation that accommodates multiple glycans. Significance: The structure provides a template for engineering E2 to elicit protective antibodies able to overcome glycosylation shifting. Hepatitis C virus (HCV) is a major cause of liver cirrhosis and hepatocellular carcinoma. A challenge for HCV vaccine development is to identify conserved epitopes able to elicit protective antibodies against this highly diverse virus. Glycan shielding is a mechanism by which HCV masks such epitopes on its E2 envelope glycoprotein. Antibodies to the E2 region comprising residues 412–423 (E2412–423) have broadly neutralizing activities. However, an adaptive mutation in this linear epitope, N417S, is associated with a glycosylation shift from Asn-417 to Asn-415 that enables HCV to escape neutralization by mAbs such as HCV1 and AP33. By contrast, the human mAb HC33.1 can neutralize virus bearing the N417S mutation. To understand how HC33.1 penetrates the glycan shield created by the glycosylation shift to Asn-415, we determined the structure of this broadly neutralizing mAb in complex with its E2412–423 epitope to 2.0 Å resolution. The conformation of E2412–423 bound to HC33.1 is distinct from the β-hairpin conformation of this peptide bound to HCV1 or AP33, because of disruption of the β-hairpin through interactions with the unusually long complementarity-determining region 3 of the HC33.1 heavy chain. Whereas Asn-415 is buried by HCV1 and AP33, it is solvent-exposed in the HC33.1-E2412–423 complex, such that glycosylation of Asn-415 would not prevent antibody binding. Furthermore, our results highlight the structural flexibility of the E2412–423 epitope, which may serve as an immune evasion strategy to impede induction of antibodies targeting this site by reducing its antigenicity.
A Proline-Tryptophan Turn in the Intrinsically Disordered Domain 2 of NS5A Protein Is Essential for Hepatitis C Virus RNA Replication*

Background: The intrinsically disordered domain 2 of NS5A is required for HCV replication. Results: We characterized a short structural motif in the domain 2 of NS5A. Conclusion: This structural motif in NS5A-D2 is essential for RNA replication. Significance: This work provides a molecular basis for further understanding of the function of the intrinsically disordered domain 2 of HCV NS5A protein. Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) and its interaction with the human chaperone cyclophilin A are both targets for highly potent and promising antiviral drugs that are in the late stages of clinical development. Despite its high interest in regards to the development of drugs to counteract the worldwide HCV burden, NS5A is still an enigmatic multifunctional protein poorly characterized at the molecular level. NS5A is required for HCV RNA replication and is involved in viral particle formation and regulation of host pathways. Thus far, no enzymatic activity or precise molecular function has been ascribed to NS5A that is composed of a highly structured domain 1 (D1), as well as two intrinsically disordered domains 2 (D2) and 3 (D3), representing half of the protein. Here, we identify a short structural motif in the disordered NS5A-D2 and report its NMR structure. We show that this structural motif, a minimal Pro314–Trp316 turn, is essential for HCV RNA replication, and its disruption alters the subcellular distribution of NS5A. We demonstrate that this Pro-Trp turn is required for proper interaction with the host cyclophilin A and influences its peptidyl-prolyl cis/trans isomerase activity on residue Pro314 of NS5A-D2. This work provides a molecular basis for further understanding of the function of the intrinsically disordered domain 2 of HCV NS5A protein. In addition, our work highlights how very small structural motifs present in intrinsically disordered proteins can exert a specific function.
Exploring the Learning Process on a Role-Emerging Practice Placement: A Qualitative Study

Two second-year occupational therapy students undertook a role-emerging placement (REP) — their third of four professional practice placements — at a therapeutic community with no on-site occupational therapy service. A qualitative study exploring the nature of the learning on this REP shows how deep learning took place and how this enabled the students to gain a strong sense of their own developing professional knowledge and skills. This report also highlights that the students' specific occupational therapy input made a unique contribution to the community's work, a view validated by the therapeutic community's own staff.
Bir Eğitim ve Araştırma Devlet Hastanesinde Ortopedistlerin Rejyonal Anestezi ile İlgili Tutum ve Bilgilerinin Değerlendirilmesi

Objective: We conducted a survey to understand the surgical behaviour and knowledge regarding regional anesthesia among orthopedic surgeons working in a training and research state hospital. Material and Methods: Anesthetic preferences were determined for hypothetical surgical procedures (total knee replacement, total hip replacement, shoulder arthroscopy, trigger finger, knee arthroscopy), both patient and for the surgeon. A 5-point Likert scale of aggrement examined perceptions of regional anesthesia. Results: We reached to 52 orthopedic surgeon (96.3%). The common reasons for favoring regional anesthesia were less postoperative sedation/confusion (76.9%), safety (75%) and less complication (67.3). Longer anesthesia performing time (61.5%) and anxiety for patients (55.8%) were reasons for not favoring regional anesthesia. Orthopedic surgeons appear to be aware of the many advantages that regional anesthesia can provide. However, both blood transfusion and deep venous thrombosis are common in the orthopedic surgical population, and it is disappointing that there was not stronger agreement of benefit in these areas. Conclusion: This survey showed that orthopedic surgeons working our hospital are supporting regional anesthesia. Barriers to increased popularity include perceived operating room delays and anxiety of patient. These issues can be solved with operating room personel education, improvements in training.
Amyloid Assemblies of Influenza A Virus PB1-F2 Protein Damage Membrane and Induce Cytotoxicity*

PB1-F2 is a small accessory protein encoded by an alternative open reading frame in PB1 segments of most influenza A virus. PB1-F2 is involved in virulence by inducing mitochondria-mediated immune cells apoptosis, increasing inflammation, and enhancing predisposition to secondary bacterial infections. Using biophysical approaches we characterized membrane disruptive activity of the full-length PB1-F2 (90 amino acids), its N-terminal domain (52 amino acids), expressed by currently circulating H1N1 viruses, and its C-terminal domain (38 amino acids). Both full-length and N-terminal domain of PB1-F2 are soluble at pH values ≤6, whereas the C-terminal fragment was found soluble only at pH ≤ 3. All three peptides are intrinsically disordered. At pH ≥ 7, the C-terminal part of PB1-F2 spontaneously switches to amyloid oligomers, whereas full-length and the N-terminal domain of PB1-F2 aggregate to amorphous structures. When incubated with anionic liposomes at pH 5, full-length and the C-terminal part of PB1-F2 assemble into amyloid structures and disrupt membrane at nanomolar concentrations. PB1-F2 and its C-terminal exhibit no significant antimicrobial activity. When added in the culture medium of mammalian cells, PB1-F2 amorphous aggregates show no cytotoxicity, whereas PB1-F2 pre-assembled into amyloid oligomers or fragmented nanoscaled fibrils was highly cytotoxic. Furthermore, the formation of PB1-F2 amyloid oligomers in infected cells was directly reflected by membrane disruption and cell death as observed in U937 and A549 cells. Altogether our results demonstrate that membrane-lytic activity of PB1-F2 is closely linked to supramolecular organization of the protein.
The relationship between perceived clinical decision making ability and medication dosage calculation ability of registered nurses

OF DISSERTATION GRADUATE SCHOOL, UNIVERSITY OF ALABAMA AT BIRMINGHAM Degree D.S. N. Program Educator o f Nursing____________________________ Name o f Candidate Lvnn M. Stover___________________________________________ Committee Chairs Lvn Reillv_________________________________________________ Title The Relationship Between Perceived Clinical Decision Malang Ability and______ Medication Dosage Calculation Ability o f Registered Nurses__________________ To be an effective registered nurse, one must be able to integrate clinical decision­ making skills into the medication calculation process in order to provide safe and effective care. Medication errors have been associated with negative outcomes for both patients and registered nurses. The execution of clinical decision-making skills throughout the medication administration process is crucial; however, the literature has not revealed a linking o f these 2 concepts. The purpose o f this study was to describe the relationship between registered nurses’ clinical decision-making skills and the accuracy o f medication dosage calculation. Simon’s (1977) theory o f decision making served as the conceptual framework for this study. The sample was composed o f 64 pediatric registered nurses who were participating in a nursing orientation program at a pediatric acute care institution. Each subject completed a demographic data instrument, the Clinical Decision Making in Nursing Scale (CDMNS) (Jenkins, 1983), and a Medication Calculation Test (MCT). The majority o f the sample were female, employed full-time, and had earned a baccalaureate degree in nursing.
Factors Affecting Mortality in Mehsana Buffalo Calves

The study was conducted on Mehsana Buffalo calf mortality at Livestock Research Station, Sardarkrushinagar Dantiwada Agricultural University. Records of 70 calves died during the period 1998–2008 were used for the said study. The deaths were more in monsoon followed by winter and least in summer. The mortality was higher in the male as compared to the female calves. The mortality percentage reduce with age advancement, the maximum being during first month of the age. The predominant causes of mortality were Calf Scour (diarrhoea), pneumonia and pneumoenteritis.
The Dendritic Cell Major Histocompatibility Complex II (MHC II) Peptidome Derives from a Variety of Processing Pathways and Includes Peptides with a Broad Spectrum of HLA-DM Sensitivity*

The repertoire of peptides displayed in vivo by MHC II molecules derives from a wide spectrum of proteins produced by different cell types. Although intracellular endosomal processing in dendritic cells and B cells has been characterized for a few antigens, the overall range of processing pathways responsible for generating the MHC II peptidome are currently unclear. To determine the contribution of non-endosomal processing pathways, we eluted and sequenced over 3000 HLA-DR1-bound peptides presented in vivo by dendritic cells. The processing enzymes were identified by reference to a database of experimentally determined cleavage sites and experimentally validated for four epitopes derived from complement 3, collagen II, thymosin β4, and gelsolin. We determined that self-antigens processed by tissue-specific proteases, including complement, matrix metalloproteases, caspases, and granzymes, and carried by lymph, contribute significantly to the MHC II self-peptidome presented by conventional dendritic cells in vivo. Additionally, the presented peptides exhibited a wide spectrum of binding affinity and HLA-DM susceptibility. The results indicate that the HLA-DR1-restricted self-peptidome presented under physiological conditions derives from a variety of processing pathways. Non-endosomal processing enzymes add to the number of epitopes cleaved by cathepsins, altogether generating a wider peptide repertoire. Taken together with HLA-DM-dependent and-independent loading pathways, this ensures that a broad self-peptidome is presented by dendritic cells. This work brings attention to the role of “self-recognition” as a dynamic interaction between dendritic cells and the metabolic/catabolic activities ongoing in every parenchymal organ as part of tissue growth, remodeling, and physiological apoptosis.
On Searching Zimin Patterns

In the area of pattern avoidability the central role is played by special words called Zimin patterns. The symbols of these patterns are treated as variables and the rank of the pattern is its number of variables. Zimin type of a word $x$ is introduced here as the maximum rank of a Zimin pattern matching $x$. We show how to compute Zimin type of a word on-line in linear time. Consequently we get a quadratic time, linear-space algorithm for searching Zimin patterns in words. Then we how the Zimin type of the length $n$ prefix of the infinite Fibonacci word is related to the representation of $n$ in the Fibonacci numeration system. Using this relation, we prove that Zimin types of such prefixes and Zimin patterns inside them can be found in logarithmic time. Finally, we give some bounds on the function $f(n,k)$ such that every $k$-ary word of length at least $f(n,k)$ has a factor that matches the rank $n$ Zimin pattern.