On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry

Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS³)-cross-linked human serum albumin (HSA) and evaluated how reproducible cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community, we developed a workflow that integrates the established software tools MaxQuant for spectra preprocessing, Xi for cross-linked peptide identification, and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 124 were subsequently quantified across 10 analyses with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides. Graphical Abstract ᅟ.

Persistently Elevated Levels of von Willebrand Factor Antigen in HIV Infection

Levels of circulating von Willebrand factor (vWf) antigen are thought to reflect endothelial involvement in various disorders. In the present study we found markedly elevated plasma levels of vWf in HIV-infected patients demonstrated on both cross-sectional and longitudinal testing. Notably, we found that a persistent rise in vWf antigen was associated with progression of HIV-related disease. This elevation of vWf antigen represented functionally normal vWf as evaluated by plasma FVIII, ristocetin cofactor assay and vWf multimer analyses. While HIV-infected patients showed enhanced platelet activation, platelets did not contribute substantially to the increased vWf levels. The high vWf levels were significantly correlated with high viral load, and during HAART, the pronounced decline in HIV RNA levels was accompanied by a corresponding decrease in vWf. The persistent elevation of functionally normal vWf during HIV infection, most probably reflecting a persistent endothelial cell activation, may have an important role in the pathogenesis of HIV infection.

Increased thalamic resting-state connectivity as a core driver of LSD-induced hallucinations

OBJECTIVE

It has been proposed that the thalamocortical system is an important site of action of hallucinogenic drugs and an essential component of the neural correlates of consciousness. Hallucinogenic drugs such as LSD can be used to induce profoundly altered states of consciousness, and it is thus of interest to test the effects of these drugs on this system.

METHOD

100 μg LSD was administrated orally to 20 healthy participants prior to fMRI assessment. Whole brain thalamic functional connectivity was measured using ROI-to-ROI and ROI-to-voxel approaches. Correlation analyses were used to explore relationships between thalamic connectivity to regions involved in auditory and visual hallucinations and subjective ratings on auditory and visual drug effects.

RESULTS

LSD caused significant alterations in all dimensions of the 5D-ASC scale and significantly increased thalamic functional connectivity to various cortical regions. Furthermore, LSD-induced functional connectivity measures between the thalamus and the right fusiform gyrus and insula correlated significantly with subjective auditory and visual drug effects.

CONCLUSION

Hallucinogenic drug effects might be provoked by facilitations of cortical excitability via thalamocortical interactions. Our findings have implications for the understanding of the mechanism of action of hallucinogenic drugs and provide further insight into the role of the 5-HT_2A -receptor in altered states of consciousness.

Phase Locking the Spin Precession in a Storage Ring

This Letter reports the successful use of feedback from a spin polarization measurement to the revolution frequency of a 0.97  GeV/c bunched and polarized deuteron beam in the Cooler Synchrotron (COSY) storage ring in order to control both the precession rate (≈121  kHz) and the phase of the horizontal polarization component. Real time synchronization with a radio frequency (rf) solenoid made possible the rotation of the polarization out of the horizontal plane, yielding a demonstration of the feedback method to manipulate the polarization. In particular, the rotation rate shows a sinusoidal function of the horizontal polarization phase (relative to the rf solenoid), which was controlled to within a 1 standard deviation range of σ=0.21  rad. The minimum possible adjustment was 3.7 mHz out of a revolution frequency of 753 kHz, which changes the precession rate by 26  mrad/s. Such a capability meets a requirement for the use of storage rings to look for an intrinsic electric dipole moment of charged particles.

Oro-facial impairment in stroke patients

Stroke is considered one of the leading causes of death and acquired disability with a peak prevalence over the age of 80 years. Stroke may cause debilitating neurological deficiencies that frequently result in sensory deficits, motor impairment, muscular atrophy, cognitive deficits and psychosocial impairment. Oro-facial impairment may occur due to the frequent involvement of the cranial nerves' cortical representation areas, central nervous system pathways or motoneuron pools. The aim of this narrative, non-systematic review was to discuss the implications of stroke on oro-facial functions and oral health-related quality of life (OHRQoL). Stroke patients demonstrate an impaired masticatory performance, possibly due to reduced tongue forces and disturbed oral sensitivity. Furthermore, facial asymmetry is common, but mostly discrete and lip restraining forces are reduced. Bite force is not different between the ipsi- and contra-lesional side. In contrast, the contra-lesional handgrip strength and tongue-palate contact during swallowing are significantly impaired. OHRQoL is significantly reduced mainly because of the functional impairment. It can be concluded that impaired chewing efficiency, dysphagia, facial asymmetry, reduced lip force and OHRQoL are quantifiable symptoms of oro-facial impairment following a stroke. In the absence of functional rehabilitation, these symptoms seem not to improve. Furthermore, stroke affects the upper limb and the masseter muscle differently, both, at a functional and a morphological level. The rehabilitation of stroke survivors should, therefore, also seek to improve the strength and co-ordination of the oro-facial musculature. This would in turn help improve OHRQoL and the masticatory function, subsequently preventing weight loss and malnutrition.

Oral tactile sensitivity and masticatory performance are impaired in stroke patients

Oro-facial impairment following stroke frequently involves reduced chewing performance, that is oral phase dysphagia. The aim was to investigate the sensitivity of oral tissues following stroke and its potential impact on masticatory function. Therefore, hospitalised post-stroke patients were recruited and compared to healthy controls. Outcome measures comprised masticatory performance employing a colour-mixing ability, that is a bolus-kneading test, maximum lip- and bite force and the one-point and two-point tactile thresholds. Food hoarding and prevalence of dry mouth were evaluated with ordinal scales. Twenty-seven stroke patients (age 64·3 ± 14·1 years) and 27 healthy controls (age 60·8 ± 14·3 years, P = 0·254) participated in this study. The groups had similar numbers of occluding units. Stroke patients reported more frequently dry mouth sensations and food hoarding. The intra-oral tactile sensitivity on the contra-lesional side was significantly lower in stroke patients compared to controls (0·0001 < P < 0·0002), and significant intra-group side differences were found only in the stroke group (0·0001 < P < 0·0010). For the lip, both sides were less sensitive in the stroke group compared with controls. The experiments confirmed lower masticatory performance and lip force in the stroke group, but the bite force was similar compared to healthy controls. Oral sensitivity was correlated with masticatory performance when a global correlation model was applied. A stroke may affect the sensitivity of the intra-oral tissues contra-lesionally, thus potentially affecting chewing function. Rehabilitation should therefore not only focus on motor impairment, but equally stimulate the sensitivity of the oral tissues, employing dry ice application or similar specific treatments.

Palatal morphology changes in post-stroke patients measured by geometric morphometrics

This study aimed to describe longitudinal palatal shape changes in post-stroke patients when compared to a sample of healthy subjects through linear measurements and geometric morphometrics. The 3D palatal scanned models of seven stroke patients having a 1-year post-stroke follow-up were matched with seven control subjects of the same age group (range 50-87 years). Intercanine, intermolar distances and palatal height were measured. 3D images were also analysed through geometric morphometrics to assess changes in the shape of the palate from T0 to T1 (1 year after the stroke). Principal component analysis was used to describe shape morphology changes, and visual colour maps were used to qualitatively assess differences between T0 and T1. No changes were detected nor in linear measures neither in palatal shape in healthy subjects from T0 to T1. The palates of stroke patients showed no linear differences either. However, when visualising shape changes through colour maps, the lateral aspects of the palatal vault were slightly narrower in T1, with respect to T0 in stroke patients. This may be attributed to altered tongue function following the stroke.

Evidence gaps in ENT surgery - a qualitative survey

Introduction: As in other disciplines, the burgeoning knowledge in ENT medicine long ago surpassed our ability to adequately absorb it and maintain a proper overview. This can give rise to actual or assumed evidence gaps that can impede the progress of the discipline and evidence-based treatment of patients. Clinics and medical practices also hold to traditional doctrines that shape day-to-day medicine, without these schools being challenged based on evidence.

Methods: Between February and June 2015, 160 ENT clinics, including 34 university hospitals, and 2,670 ENT practices took part in a two-arm online survey on existing or perceived evidentiary gaps in ENT medicine using a previously developed questionnaire. The survey used for half of the participants was open in form; the other half were given a closed survey with systematics of the field for orientation. The survey was augmented with additional data such as the number of publications and focus areas in the clinics and the age and type of practice of the established physicians.

Results: The return rate from the clinics was 39.7%; the return rate of the closed surveys was 29.3%. Of the physicians in medical practice, 14.6% responded to the closed and 18.6% to the open survey. There were no major differences between the two forms of survey. Otological and oncological issues comprised approximately 30% of the list of answers from clinics. Corresponding questions were formulated regarding the current diagnostic and therapeutic problems, such as with stage-related tumor treatment or implantable hearing aids. Diagnostic procedures, e.g., special new procedures in audiology and vestibulogy, dominated the surveys from the practices. However clinics and practices alike cited marginal areas of the discipline that are of daily relevance.

Discussion: The cited evidence gaps then needed to be verified or refuted and clarified based on research of the literature as to whether the existing evidence actually reached healthcare providers in the form of guidelines, publications, conferences, or continuing training for application in daily practice. Other steps would include prioritizing future research, evidence mapping, deciding on further systematic reviews, and targeted studies in conjunction with procuring third-party funding and in cooperation with patient associations. The knowledge thus gained should ultimately be transferred in improved form for application in daily clinical practice. Ten questions of key importance each needed to be formulated for the hospitals and practices.

The "killer cell story" in recurrent miscarriage: Association between activated peripheral lymphocytes and uterine natural killer cells

Peripheral and uterine NK cells (pNK, uNK) can be distinguished according to their receptor expression. Recent studies indicate an association of elevated pNK and uNK with recurrent miscarriage (RM). This study aimed to analyze pNK and uNK in patients with RM and healthy controls. Out of n=590 RM patients screened according to a standard diagnostic protocol, n=268 couples with ≥3 consecutive RM were identified. Subgroups consisted of n=151 primary RM (pRM), n=85 secondary RM (sRM), n=32 tertiary RM (tRM) and n=42 healthy controls. Finally, n=147 idiopathic RM (iRM) and n=121 non-iRM patients were identified. Peripheral blood levels of CD45+CD3-CD56+CD16+ NK cells were determined in non-pregnant patients and controls in the mid-luteal phase by FACS. In n=129 RM patients a uterine biopsy was taken to evaluate CD56+ NK cells by immunohistochemistry. PRM showed higher absolute pNK than sRM (median/μl (Q1;Q3): 234 (147;306) vs 176 (128;245), p=0.02). Further a trend towards higher pNK percentages in pRM was detected. UNK numbers did not differ between RM subgroups and did not correlate with pNK. However, the rate of highly elevated uNK was increased in iRM compared to non-iRM patients (p=0.04). Further, higher numbers of CD45+CD3-DR+ (p<0.01) and CD45+CD3+CD8+DR+ (p=0.04) peripheral lymphocytes were associated with higher uNK numbers. In conclusion, elevated pNK were present in pRM patients. Although pNK and uNK numbers did not correlate, the association between high CD45+CD3-DR+ and CD45+CD3+CD8+DR+ peripheral lymphocytes and uNK might indicate that activated NK, B and T cells provide cytokines for the differentiation of uNK.

Peri-implant femoral fractures: The risk is more than three times higher within PFN compared with DHS

INTRODUCTION

Information is lacking regarding incidence rates, treatment regimens, and outcomes concerning peri-implant femoral fractures (PIF). Therefore, we performed a retrospective study to provide scientific data concerning incidence and outcome of PIF following osteosynthesis of proximal femoral fractures (PFF).

MATERIAL AND METHODS

We retrospectively included all patients who received osteosynthesis for PFF between 2006 and 2015 and in whom PIF was confirmed postoperatively. All available patients with PIF were contacted minimum one year post-surgery.

RESULTS

A total of 1314 osteosynthesis procedures were performed, of which 705 were proximal femoral nails (PFNs), 597 were dynamic hip screws (DHSs), and 12 were screws appliances only. During the same period, 18 PIFs (1.4%) were reported. However, PIF was 3.7 times higher within PFN when compared to DHS (15/705:2.1% versus 3/597:0.5%; odds ratio: 3.7). The following analysis also included 8 patients with PIF who were referred from other hospitals, resulting in a total of 26 patients. Mean patient age was 84.8 years (range, 57-95), with a predominance in female (23×) and in the left femur (19×). PIF occurred after an average of 23.6 months (range, 1-81) post-surgery. The fractures, most of which were spiral-shaped, were most commonly treated with locking plate osteosynthesis. The surgical revision rate was 7.7%, and the one-year mortality was 23.1%. At an average of 43.0 months (range, 12-100) post-surgery, it was possible to contact 18/26 patients (69.2%), and their mean Parker Mobility Score was 5.2 points (range 2-9).

CONCLUSIONS

Peri-implant femoral fracture is a rare incident within the old age traumatology of PFF. However, based on our small number of cases, it occurred within PFN much more frequently compared with DHS. Locking plate osteosynthesis has been shown to be effective and reliable. Surgical revision and mortality rates do not appear to be increased when compared to those with the initial treatment of proximal femoral fractures.

How to Reach a Thousand-Second in-Plane Polarization Lifetime with 0.97-GeV/c Deuterons in a Storage Ring

We observe a deuteron beam polarization lifetime near 1000 s in the horizontal plane of a magnetic storage ring (COSY). This long spin coherence time is maintained through a combination of beam bunching, electron cooling, sextupole field corrections, and the suppression of collective effects through beam current limits. This record lifetime is required for a storage ring search for an intrinsic electric dipole moment on the deuteron at a statistical sensitivity level approaching 10^{-29}  e cm.

Pharmacokinetic Evaluation of a Drug Transporter Cocktail Consisting of Digoxin, Furosemide, Metformin, and Rosuvastatin

This article reports the clinical investigation of a probe drug cocktail containing substrates of key drug transporters. Single oral doses of 0.25 mg digoxin (P-gp), 5 mg furosemide (OAT1 and OAT3), 500 mg metformin (OCT2, MATE1, and MATE2-K), and 10 mg rosuvastatin (OATP1B1, OATP1B3, and BCRP) were administered separately or as a cocktail in a randomized six-period crossover trial in 24 healthy male volunteers. As a cocktail, relative bioavailabilities of digoxin and metformin and furosemide AUC0-tz were similar to separate dosing. However, when administered as a cocktail the Cmax of furosemide was 19.1% lower and the Cmax and AUC0-tz of rosuvastatin were 38.6% and 43.4% higher, respectively. In addition, the effects of increased doses of metformin or furosemide on the cocktail were investigated in 11 and 12 subjects, respectively. The cocktail explored in this trial has the potential to be used for the in vivo screening of transporter-mediated drug-drug interactions. © 2016 American Society for Clinical Pharmacology and Therapeutics.

Transcriptional Regulation During Zygotic Genome Activation in Zebrafish and Other Anamniote Embryos

Embryo development commences with the fusion of two terminally differentiated haploid gametes into the totipotent fertilized egg, which through a series of major cellular and molecular transitions generate a pluripotent cell mass. The activation of the zygotic genome occurs during the so-called maternal to zygotic transition and prepares the embryo for zygotic takeover from maternal factors, in the control of the development of cellular lineages during differentiation. Recent advances in next generation sequencing technologies have allowed the dissection of the genomic and epigenomic processes mediating this transition. These processes include reorganization of the chromatin structure to a transcriptionally permissive state, changes in composition and function of structural and regulatory DNA-binding proteins, and changeover of the transcriptome as it is overhauled from that deposited by the mother in the oocyte to a zygotically transcribed complement. Zygotic genome activation in zebrafish occurs 10 cell cycles after fertilization and provides an ideal experimental platform for elucidating the temporal sequence and dynamics of establishment of a transcriptionally active chromatin state and helps in identifying the determinants of transcription activation at polymerase II transcribed gene promoters. The relatively large number of pluripotent cells generated by the fast cell divisions before zygotic transcription provides sufficient biomass for next generation sequencing technology approaches to establish the temporal dynamics of events and suggest causative relationship between them. However, genomic and genetic technologies need to be improved further to capture the earliest events in development, where cell number is a limiting factor. These technologies need to be complemented with precise, inducible genetic interference studies using the latest genome editing tools to reveal the function of candidate determinants and to confirm the predictions made by classic embryological tools and genome-wide assays. In this review we summarize recent advances in the characterization of epigenetic regulation, transcription control, and gene promoter function during zygotic genome activation and how they fit with old models for the mechanisms of the maternal to zygotic transition. This review will focus on the zebrafish embryo but draw comparisons with other vertebrate model systems and refer to invertebrate models where informative.

[Gaps of Evidence in ENT-Surgery - a Qualitative Survey]

INTRODUCTION

As in other disciplines, the burgeoning knowledge in ENT medicine long ago surpassed our ability to adequately absorb it and maintain a proper overview. This can give rise to actual or assumed knowledge gaps that can impede the progress of the discipline and evidence-based treatment of patients. Clinics and medical practices also hold to traditional doctrines that shape day-to-day medicine, without these schools being challenged based on evidence.

METHODS

Between February and June 2015, 160 ENT clinics, including 34 university hospitals, and 2,670 ENT practices took part in a two-arm online survey on existing or perceived evidentiary gaps in ENT medicine using a previously development questionnaire. The survey used for half the participants was open in form; the other half were given a closed survey with systematics of the field for orientation. The survey was augmented with additional data such as the number of publications and focus areas in the clinics and the age and type of practice of the established physicians.

RESULTS

The return rate from the clinics was 39.7%; the return rate of the closed surveys was 29.3%. Of the physicians in medical practice, 14.6% responded to the closed and 18.6% to the open survey. There were no major differences between the two forms of survey. Otological and oncological issues comprised approximately 30% of the list of answers from clinics. Corresponding questions were formulated regarding the current diagnostic and therapeutic problems, such as with stage-related tumor treatment or implantable hearing aids. Diagnostic procedures, e.g., special new procedures in audiology and vestibulogy, dominated the surveys from the practices. However clinics and practices alike cited marginal areas of the discipline that are of daily relevance.

DISCUSSION

The cited knowledge gaps then needed to be verified or refuted and clarified based on research of the literature as to whether the existing evidence actually reached healthcare providers in the form of guidelines, publications, conferences or continuing training for application in daily practice. Other steps would include prioritizing future research, evidence mapping, deciding on further systematic reviews, and targeted studies in conjunction with procuring third-party funding and in cooperation with patient associations. The knowledge thus gained should ultimately be transferred in improved form for application in daily clinical practice. Ten questions of key importance each needed to be formulated for the hospitals and practices.