bluuebunny/crossref_metadata_2025 huggingface dataset:
The Healthcare Cost of Mandibular Nonunions
Authors: Lee Kevin C. , Chuang Sung-Kiang , Koch Alia
Published: July 2019

The aim of this retrospective cohort study was to compare the costs and characteristics between isolated mandible fractures and mandibular nonunions. From October 2015 to December 2016, the National Inpatient Sample (NIS) was searched for patients admitted with a primary diagnosis of a mandible fracture. The sample was divided between those admitted for an initial evaluation of an isolated fracture and a fracture nonunion. Demographic descriptors, injury characteristics, and inpatient factors were recorded. A total of 1432 patients were included in the final sample, of whom 51 (3.6%) were admitted for a nonunion. Nonunion patients were significantly older (P < 0.01), and nonunions were more often localized to the body (24 vs 11%; P = 0.02). Compared to that of isolated fractures, a greater proportion of nonunions required open reduction and internal fixation (86 vs 59%; P < 0.01) and bone grafting (37 vs 1.4%; P < 0.01), and nonunions imparted +32.6% greater hospitals costs (median: $10,680 vs 14,162; P < 0.01). In conclusion, compared to isolated mandible fractures, mandibular nonunions occurred in older patients, had a higher frequency in body of the mandible, and utilized significantly more hospital resources per admission.
Application of a Layered Muscle Flap Technique for the Reconstruction of the Cupid's Bow and Vermilion in the Repair of Secondary Cleft Lip Deformities
Authors: Ma Hengyuan , Zhang Nong , Yin Ningbei , Guo Bin
Published: July 2019

In the repair of unilateral cleft lip, the Cupid's bow, and vermilion on the affected side are sometimes lowered excessively. Methods involving skin and mucosa flaps have been used to correct this issue, but they pose some risk of scarring. The authors here describe a layered muscle flap technique that was based on the anatomical research of nasal-labial muscles, especially the levator labii superioris alaeque nasi muscle. This technique can be used to suspend the Cupid's bow and vermilion in secondary unilateral cleft lip repair. Forty-five patients with secondary unilateral cleft lip with excessively lowered Cupid's bows and vermilion on the affected side were included in this study, which lasted 3 years. These patients were treated using the layered muscle flap surgical technique. The heights of specific bilateral landmarks were measured on patient photos and used to define the symmetry of bilateral Cupid's bow and vermilion. The comparison between post-operative and pre-operative symmetries was used to evaluate the post-operative results, and most of them were satisfactory. The results were also mostly well retained in follow-up investigations. This layered muscle flap technique could be effective in selected cases.
Comparison of the Preference of Nutritional Support for Patients With Severe Acute Pancreatitis
Authors: Hui Liangliang , Zang Kui , Wang Min , Shang Futai , Zhang Guoxin
Published: July 2019

This study aimed to compare the preference of different methods of nutritional support for patients with severe acute pancreatitis (SAP). Patients with SAP were divided into the enteral nutrition group (EN group, 16 cases), total the parenteral nutrition group (TPN group, 14 cases), and the enteral plus total parenteral nutrition group (EN+TPN group, 15 cases). At 7 days after admisson, TPN and EN+TPN groups showed significantly increased Ranson scores compared with the EN group (p < .05). At 14 and 21 days after admisson, TPN and EN+TPN groups exhibited significantly increased Acute Physology and Chronic Health Evaluation (APACHE) II scores, Ranson scores, and intra-abdominal pressure compared with the EN group (p < .05 or p < .01). The incidences of multiple organ dysfunction syndrome and its complication in the EN group were significantly lower than the TPN and EN+TPN groups (p < .05). Hospital stay was significantly lower, but the incidences of abdominal distenson and regurgitation complications were significantly higher in the EN group than in the TPN and EN+TPN groups (p < .05). In concluson, early enteral nutrition could significantly improve nutritional status of patients with SAP, shorten the course of the disease, and reduce the incidences of infection, death, and complication, but also increase the risk of abdominal distenson and regurgitation.
Differences in Factors Affecting the Quality of Life Over Time After the Gastrectomy in Patients With Stage I Gastric Cancer
Authors: Lee Kyung Eun , Lim Kyung Hee
Published: July 2019

Patients with Stage I gastric cancer experience decreased postgastrectomy quality of life (QoL) despite the excellent surgical outcomes. We need to find foundational data required to develop effective nursing care plans designed to improve their QoL. This study examined QoL of patients with Stage I gastric cancer over time following gastrectomy and the effects of QoL subdomains on the patients' overall QoL over time after surgery. Data were collected from 138 patients with Stage I gastric cancer who had undergone gastrectomy within the previous 3 years. Data were classified into 3 groups according to the length of postsurgery time: 12 months or less (Group 1), 13–24 months (Group 2), and 25–36 months (Group 3). A confirmatory factor analysis was performed to examine the effects of QoL subdomains. Quality of life of patients with Stage I gastric cancer improves over time following gastrectomy. Postoperative physical symptoms influenced QoL most in Group 1 patients, whereas physical well-being and emotional well-being were the highest contributors to QoL in Groups 2 and 3, respectively. Nursing interventions must be tailored to meet the particular needs of patients at each period of recovery in order to improve QoL of patients with Stage I gastric cancer after a gastrectomy.
Transition from abdominal aortic and junctional tourniquet to zone 3 resuscitative endovascular balloon occlusion of the aorta is feasible with hemodynamic support after porcine class IV hemorrhage
Authors: Brännström Andreas , Dahlquist Albin , Gustavsson Jenny , Arborelius Ulf P. , Günther Mattias
Published: July 2019

BACKGROUND

Traumatic hemorrhage remains a major cause of death in rural civilian and combat environments. Potential interventions to control hemorrhage from the pelvis and lower junctional regions include the abdominal aortic and junctional tourniquet (AAJT) and resuscitative endovascular balloon occlusion of the aorta (REBOA). The AAJT requires low technical skills and may thus be used by nonmedical professionals, but is associated with time-dependent ischemic complications. In combination with delayed patient evacuation, it may therefore be deleterious. Transition to zone 3 REBOA in higher levels of care may be a possibility to maintain hemostasis, mitigate adverse effects and enable surgery in patients resuscitated with the AAJT. It is possible that a transition between the interventions could lead to hemodynamic penalties. Therefore, we investigated the feasibility of replacing the AAJT with zone 3 REBOA in a porcine model of uncontrolled femoral hemorrhage.

METHODS

Domestic pigs (n = 12) averaging 57 kg were exposed to a class IV uncontrolled hemorrhage from the common femoral artery. The animals were randomized to 60-minute AAJT (n = 6) or 30-minute AAJT with transition to 30-minute zone 3 REBOA. Hemodynamic and metabolic parameters and ultrasonographic measurements of the common femoral artery were collected.

RESULTS

Transition from AAJT to zone 3 REBOA caused a significant decrease in mean arterial pressure (25 mm Hg). Hemostasis was maintained. The common femoral artery diameter decreased by 1.8 mm (38%) after hemorrhage and further 0.7 mm (23%) after aortic occlusion.

CONCLUSION

Transition from AAJT to zone 3 REBOA after a class IV bleeding is feasible with hemodynamic support. Vascular access to the femoral artery for REBOA insertion poses a technical challenge after hemorrhage and AAJT application.

LEVEL OF EVIDENCE

Laboratory animal study, level IV.
Hypoxia/reoxygenation decreases endothelial glycocalyx via reactive oxygen species and calcium signaling in a cellular model for shock
Authors: Jackson-Weaver Olan , Friedman Jessica K. , Rodriguez Laura A. , Hoof Marcus A. , Drury Robert H. , Packer Jacob T. , Smith Alison , Guidry Chrissy , Duchesne Juan C.
Published: July 2019

BACKGROUND

Ischemia/reperfusion injury (IRI) has been shown to cause endothelial glycocalyx (EG) damage.

Whether the hypoxic/ischemic insult or the oxidative and inflammatory stress of reperfusion plays a greater part in glycocalyx damage is not known. Furthermore, the mechanisms by which IRI causes EG damage have not been fully elucidated. The aims of this study were to determine if hypoxia alone or hypoxia/reoxygenation (H/R) caused greater damage to the glycocalyx, and if this damage was mediated by reactive oxygen species (ROS) and Ca2+ signaling.

METHODS

Human umbilical vein endothelial cells were cultured to confluence and exposed to either normoxia (30 minutes), hypoxia (2% O2 for 30 minutes), or H/R (30 minutes hypoxia followed by 30 minutes normoxia). Some cells were pretreated with ROS scavengers TEMPOL, MitoTEMPOL, Febuxostat, or Apocynin, or with the Ca2+ chelator BAPTA or Ca2+ channel blockers 2-aminoethoxydiphenyl borate, A967079, Pyr3, or ML204. Intracellular ROS was quantified for all groups. Endothelial glycocalyx was measured using fluorescently tagged wheat germ agglutinin and imaged with fluorescence microscopy.

RESULTS

Glycocalyx thickness was decreased in both hypoxia and H/R groups, with the decrease being greater in the H/R group. TEMPOL, MitoTEMPOL, BAPTA, and 2-aminoethoxydiphenyl borate prevented loss of glycocalyx in H/R. The ROS levels were likewise elevated compared with normoxia in both groups, but were increased in the H/R group compared with hypoxia alone. BAPTA did not prevent ROS production in either group.

CONCLUSION

In our cellular model for shock, we demonstrate that although hypoxia alone is sufficient to produce glycocalyx loss, H/R causes a greater decrease in glycocalyx thickness. Under both conditions damage is dependent on ROS and Ca2+ signaling. Notably, we found that ROS are generated upstream of Ca2+, but that ROS-mediated damage to the glycocalyx is dependent on Ca2+.
Short-term versus long-term trauma mortality: A systematic review
Authors: Frydrych Lynn M. , Keeney-Bonthrone Toby P. , Gwinn Elizabeth , Wakam Glenn K. , Anderson Maia S. , Delano Matthew J.
Published: July 2019

BACKGROUND

Trauma is the leading cause of death in the United States for persons under 44 years and the fourth leading cause of death in the elderly. Advancements in clinical care and standardization of treatment protocols have reduced 30-day trauma mortality to less than 4%. However, these improvements do not seem to correlate with long-term outcomes. Some reports have shown a greater than 20% mortality rate when looking at long-term outcomes. The aim of this study was to systematically review the incongruence between short- and long-term mortality for trauma patients.

METHODS

For this systematic review, we searched the Cochrane Library, EMBASE, Ovid Medline, Google Scholar, and Web of Science database to obtain relevant English, German, French, and Portuguese articles from 1965 to 2018.

RESULTS

Trauma patients have decreased long-term survival when compared to the general population and when compared with age-matched cohorts. Postdischarge trauma mortality is significantly higher (mean, 4.6% at 3–6 months, 15.8% at 2–3 years, 26.3% at 5–25 years) compared with controls (mean, 1.3%, 2.2%, and 15.6%, respectively). Patient comorbidities likely contribute to long-term trauma deaths. Trauma patients discharged to a skilled nursing facility have worse mortality compared with those discharged either to home or a rehabilitation center. In contrast to data available which illustrate that short-term mortality has improved, quality of evidence was not sufficient to determine if any improvements in long-term trauma mortality outcomes have also occurred.

CONCLUSIONS

The decreased short-term mortality observed in trauma patients does not appear correlated with decreased long-term mortality. The extent to which increased long-term trauma mortality is related to the initial traumatic insult—versus rising population age and comorbidity burden as well as suboptimal discharge location—requires further study.

LEVEL OF EVIDENCE

Systematic Review, level IV.
The macrophage checkpoint CD47 : SIRPα for recognition of ‘self’ cells: from clinical trials of blocking antibodies to mechanobiological fundamentals
Authors: Andrechak Jason C. , Dooling Lawrence J. , Discher Dennis E.
Published: July 2019

Immunotherapies against some solid tumour types have recently shown unprecedented, durable cures in the clinic, and the most successful thus far involves blocking inhibitory receptor ‘checkpoints’ on T cells. A similar approach with macrophages is emerging by blocking the ubiquitously expressed ‘marker of self’ CD47 from binding the inhibitory receptor SIRPα on macrophages. Here, we first summarize available information on the safety and efficacy of CD47 blockade, which raises some safety concerns with the clearance of ‘self’ cells but also suggests some success against haematological (liquid) and solid cancers. Checkpoint blockade generally benefits from parallel activation of the immune cell, which can occur for macrophages in multiple ways, such as by combination with a second, tumour-opsonizing antibody and perhaps also via rigidity sensing. Cytoskeletal forces in phagocytosis and inhibitory ‘self’-signalling are thus reviewed together with macrophage mechanosensing, which extends to regulating levels of SIRPα and the nuclear protein lamin A, which affects phenotype and cell trafficking. Considerations of such physical factors in cancer and the immune system can inform the design of new immunotherapies and help to refine existing therapies to improve safety and efficacy.

This article is part of a discussion meeting issue ‘Forces in cancer: interdisciplinary approaches in tumour mechanobiology’.
Engineering approaches to studying cancer cell migration in three-dimensional environments
Authors: Zuela-Sopilniak Noam , Lammerding Jan
Published: July 2019

Cancer is one of the most devastating diseases of our time, with 17 million new cancer cases and 9.5 million cancer deaths in 2018 worldwide. The mortality associated with cancer results primarily from metastasis, i.e. the spreading of cancer cells from the primary tumour to other organs. The invasion and migration of cells through basement membranes, tight interstitial spaces and endothelial cell layers are key steps in the metastatic cascade. Recent studies demonstrated that cell migration through three-dimensional environments that mimic the
in vivo
conditions significantly differs from their migration on two-dimensional surfaces. Here, we review recent technological advances made in the field of cancer research that provide more ‘true to the source’ experimental platforms and measurements for the study of cancer cell invasion and migration in three-dimensional environments. These include microfabrication, three-dimensional bioprinting and intravital imaging tools, along with force and stiffness measurements of cells and their environments. These techniques will enable new studies that better reflect the physiological environment found
in vivo
, thereby producing more robust results. The knowledge achieved through these studies will aid in the development of new treatment options with the potential to ultimately lighten the devastating cost cancer inflicts on patients and their families.

This article is part of a discussion meeting issue ‘Forces in cancer: interdisciplinary approaches in tumour mechanobiology’.
Is cell migration a selectable trait in the natural evolution of cancer development?
Authors: Disanza Andrea , Bisi Sara , Frittoli Emanuela , Malinverno Chiara , Marchesi Stefano , Palamidessi Andrea , Rizvi Abrar , Scita Giorgio
Published: July 2019

Selective evolutionary pressure shapes the processes and genes that enable cancer survival and expansion in a tumour-suppressive environment. A distinguishing lethal feature of malignant cancer is its dissemination and seeding of metastatic foci. A key requirement for this process is the acquisition of a migratory/invasive ability. However, how the migratory phenotype is selected for during the natural evolution of cancer and what advantage, if any, it might provide to the growing malignant cells remain open issues. In this opinion piece, we discuss three possible answers to these issues. We will examine lines of evidence from mathematical modelling of cancer evolution that indicate that migration is an intrinsic selectable property of malignant cells that directly impacts on growth dynamics and cancer geometry. Second, we will argue that migratory phenotypes can emerge as an adaptive response to unfavourable growth conditions and endow cells not only with the ability to move/invade, but also with specific metastatic traits, including drug resistance, self-renewal and survival. Finally, we will discuss the possibility that migratory phenotypes are coincidental events that emerge by happenstance in the natural evolution of cancer.

This article is part of a discussion meeting issue ‘Forces in cancer: interdisciplinary approaches in tumour mechanobiology’.
Cell migration through three-dimensional confining pores: speed accelerations by deformation and recoil of the nucleus
Authors: Krause Marina , Yang Feng Wei , te Lindert Mariska , Isermann Philipp , Schepens Jan , Maas Ralph J. A. , Venkataraman Chandrasekhar , Lammerding Jan , Madzvamuse Anotida , Hendriks Wiljan , te Riet Joost , Wolf Katarina
Published: July 2019

Directional cell migration in dense three-dimensional (3D) environments critically depends upon shape adaptation and is impeded depending on the size and rigidity of the nucleus. Accordingly, the nucleus is primarily understood as a physical obstacle; however, its pro-migratory functions by stepwise deformation and reshaping remain unclear. Using atomic force spectroscopy, time-lapse fluorescence microscopy and shape change analysis tools, we determined the nuclear size, deformability, morphology and shape change of HT1080 fibrosarcoma cells expressing the Fucci cell cycle indicator or being pre-treated with chromatin-decondensating agent TSA. We show oscillating peak accelerations during migration through 3D collagen matrices and microdevices that occur during shape reversion of deformed nuclei (recoil), and increase with confinement. During G1 cell-cycle phase, nucleus stiffness was increased and yielded further increased speed fluctuations together with sustained cell migration rates in confinement when compared to interphase populations or to periods of intrinsic nuclear softening in the S/G2 cell-cycle phase. Likewise, nuclear softening by pharmacological chromatin decondensation or after lamin A/C depletion reduced peak oscillations in confinement. In conclusion, deformation and recoil of the stiff nucleus contributes to saltatory locomotion in dense tissues.

This article is part of a discussion meeting issue ‘Forces in cancer: interdisciplinary approaches in tumour mechanobiology’.
Applicability of drug response metrics for cancer studies using biomaterials
Authors: Brooks Elizabeth A. , Galarza Sualyneth , Gencoglu Maria F. , Cornelison R. Chase , Munson Jennifer M. , Peyton Shelly R.
Published: July 2019

Bioengineers have built models of the tumour microenvironment (TME) in which to study cell–cell interactions, mechanisms of cancer growth and metastasis, and to test new therapies. These models allow researchers to culture cells in conditions that include features of the
in vivo
TME implicated in regulating cancer progression, such as extracellular matrix (ECM) stiffness, integrin binding to the ECM, immune and stromal cells, growth factor and cytokine depots, and a three-dimensional geometry more representative of the
in vivo
TME than tissue culture polystyrene (TCPS). These biomaterials could be particularly useful for drug screening applications to make better predictions of efficacy, offering better translation to preclinical models and clinical trials. However, it can be challenging to compare drug response reports across different biomaterial platforms in the current literature. This is, in part, a result of inconsistent reporting and improper use of drug response metrics, and vast differences in cell growth rates across a large variety of biomaterial designs. This study attempts to clarify the definitions of drug response measurements used in the field, and presents examples in which these measurements can and cannot be applied. We suggest as best practice to measure the growth rate of cells in the absence of drug, and follow our ‘decision tree’ when reporting drug response metrics.

This article is part of a discussion meeting issue ‘Forces in cancer: interdisciplinary approaches in tumour mechanobiology’.
Forces and constraints controlling podosome assembly and disassembly
Authors: Rafiq Nisha Bte Mohd , Grenci Gianluca , Lim Cheng Kai , Kozlov Michael M. , Jones Gareth E. , Viasnoff Virgile , Bershadsky Alexander D.
Published: July 2019

Podosomes are a singular category of integrin-mediated adhesions important in the processes of cell migration, matrix degradation and cancer cell invasion. Despite a wealth of biochemical studies, the effects of mechanical forces on podosome integrity and dynamics are poorly understood. Here, we show that podosomes are highly sensitive to two groups of physical factors. First, we describe the process of podosome disassembly induced by activation of myosin-IIA filament assembly. Next, we find that podosome integrity and dynamics depends upon membrane tension and can be experimentally perturbed by osmotic swelling and deoxycholate treatment. We have also found that podosomes can be disrupted in a reversible manner by single or cyclic radial stretching of the substratum. We show that disruption of podosomes induced by osmotic swelling is independent of myosin-II filaments. The inhibition of the membrane sculpting protein, dynamin-II, but not clathrin, resulted in activation of myosin-IIA filament formation and disruption of podosomes. The effect of dynamin-II inhibition on podosomes was, however, independent of myosin-II filaments. Moreover, formation of organized arrays of podosomes in response to microtopographic cues (the ridges with triangular profile) was not accompanied by reorganization of myosin-II filaments. Thus, mechanical elements such as myosin-II filaments and factors affecting membrane tension/sculpting independently modulate podosome formation and dynamics, underlying a versatile response of these adhesion structures to intracellular and extracellular cues.

This article is part of a discussion meeting issue ‘Forces in cancer: interdisciplinary approaches in tumour mechanobiology’.
Cooperativity between stromal cytokines drives the invasive migration of human breast cancer cells
Authors: Elisha Yair , Sagi Yael , Klein Georg , Straussman Ravid , Geiger Benjamin
Published: July 2019

The cross-talk between cancer cells and the stromal microenvironment plays a key role in regulating cancer invasion. Here, we employed an
ex vivo
invasion model system for exploring the regulation of breast cancer cells infiltration into a variety of stromal fibroblast monolayers. Our results revealed considerable variability in the stromal induction of invasiveness, with some lines promoting and others blocking invasion. It was shown that conditioned medium (CM), derived from invasion-promoting fibroblasts, can induce epithelial–mesenchymal transition-like process in the cancer cells, and trigger their infiltration into a monolayer of invasion-blocking fibroblasts. To identify the specific invasion-promoting molecules, we analysed the cytokines in stimulatory CM, screened a library of purified cytokines for invasion-promoting activity and tested the effect of specific inhibitors of selected cytokine receptors on the CM-induced invasion. Taken together, these experiments indicated that the invasiveness of BT-474 is induced by the combined action of IL1 and IL6 and that IL1 can induce IL6 secretion by invasion-blocking fibroblasts, thereby triggering cancer cell invasion into the stroma. This unexpected observation suggests that stromal regulation of cancer invasion may involve not only cross-talk between stromal and cancer cells, but also cooperation between different stromal subpopulations.

This article is part of a discussion meeting issue ‘Forces in cancer: interdisciplinary approaches in tumour mechanobiology’.
Evaluation of the RESIST-4 O.K.N.V immunochromatographic lateral flow assay for the rapid detection of OXA-48, KPC, NDM and VIM carbapenemases from cultured isolates
Authors: MacDonald James Wesley , Chibabhai Vindana
Published: July 2019

Purpose This study aimed to evaluate the performance of the RESIST-4 O.K.N.V immunochromatographic lateral flow assay for the detection of OXA-48, KPC, NDM and VIM carbapenemases in 100 clinical

Enterobacteriaceae

isolates using solid culture media.

Methodology In total, 100 clinical

Enterobacteriaceae

isolates with characterized β-lactamase enzymes (OXA-48 n=46, KPC n =4, NDM n =43 and VIM n =10) were evaluated using the RESIST-4 O.K.N.V assay. The assay was also evaluated using carbapenem-sensitive control strains and confirmed non-carbapenemase-producing

Enterobacteriaceae

clinical isolates resistant to carbapenems. Inter-rater agreement of the test was evaluated by four different users who tested 11 randomly selected isolates daily over 3 days.

Results Overall accuracy of the assay was 99.5  %. For the detection of KPC, OXA-48 and its variants and VIM the assay correctly identified 100  % of the isolates when compared to PCR. Initial performance for NDM detection was sensitivity=95.3 %, specificity=100  %. Two PCR positive

Providencia rettgeri

isolates rendered false negative results on the assay. Retesting from a carbapenem zone of inhibition rendered a positive result for both isolates increasing the sensitivity to 100  %. No false positive results or cross reactions were detected.

Conclusion The RESIST-4 O.K.N.V is reliable, sensitive and specific for the detection of OXA-48, KPC, NDM and VIM carbapenemases. Further evaluation on improving NDM detection in organisms from the Proteeae tribe is warranted to determine optimal test conditions.
Dual SMAD inhibition and Wnt inhibition enable efficient and reproducible differentiations of induced pluripotent stem cells into retinal ganglion cells
Authors: Chavali Venkata R. M. , Haider Naqi , Rathi Sonika , Vrathasha Vrathasha , Alapati Teja , He Jie , Gill Kamaljot , Nikonov Roman , Duong Thu T. , McDougald Devin S. , Nikonov Sergei , O’ Brien Joan , Mills Jason A.
Published: July 2019

Glaucoma is a group of progressive optic neuropathies that share common biological and clinical characteristics including irreversible changes to the optic nerve and visual field loss caused by death of retinal ganglion cells (RGCs). The loss of RGCs manifests as characteristic cupping or optic nerve degeneration, resulting in visual field loss in patients with Glaucoma. Published studies on in vitro RGC differentiation from stem cells utilized classical RGC signaling pathways mimicking retinal development in vivo. Although many strategies allowed for the generation of RGCs, increased variability between experiments and lower yield hampered the cross comparison between individual lines and between experiments. To address this critical need, we developed a reproducible chemically defined in vitro methodology for generating retinal progenitor cell (RPC) populations from iPSCs, that are efficiently directed towards RGC lineage. Using this method, we reproducibly differentiated iPSCs into RGCs with greater than 80% purity, without any genetic modifications. We used small molecules and peptide modulators to inhibit BMP, TGF-β (SMAD), and canonical Wnt pathways that reduced variability between iPSC lines and yielded functional and mature iPSC-RGCs. Using CD90.2 antibody and Magnetic Activated Cell Sorter (MACS) technique, we successfully purified Thy-1 positive RGCs with nearly 95% purity.
Intensity of infection with intracellularEimeriaspp. and pinworms is reduced in hybrid mice compared to parental subspecies
Authors: Balard Alice , Jarquín-Díaz Víctor Hugo , Jost Jenny , Martincová Iva , Ďureje Ľudovít , Piálek Jaroslav , Macholán Miloš , Goüy de Bellocq Joëlle , Baird Stuart J. E. , Heitlinger Emanuel
Published: July 2019

The longstanding impression that hybrid mice are more highly parasitized and therefore less fit than parentals persists despite the findings of recent studies. Working across a novel transect of the European House Mouse hybrid zone we assessed intracellular infections byEimeria, a parasite of high pathogenicity, and infections by pinworms, assumed to be less pathogenic. ForEimeriawe found lower intensities in hybrid hosts than in parental mice but no evidence of lowered probability of infection in the centre of the hybrid zone. This means ecological and epidemiological factors are very unlikely to be responsible for the reduced load of infected hybrids. Focussing on parasite intensity (load in infected hosts) we also corroborated reduced pinworm loads reported for hybrid mice in previous studies. In addition we questioned whether differences in body condition during infection would indicate different impacts on hybrid vs. parental hosts’ health. We couldn’t show such an effect. We conclude that intensity of diverse parasites, including the previously unstudiedEimeria, is reduced in hybrid mice compared to parental subspecies. We suggest caution in extrapolating this to differences in hybrid host fitness in the absence of, for example, evidence for a link between parasitemia and health.
Developing critical thinking in STEM education through inquiry-based writing in the laboratory classroom
Authors: Jeon Ah-Jung , Kellogg David , Khan Mohammed Asif , Tucker-Kellogg Greg
Published: July 2019

Laboratory pedagogy is moving away from step-by-step instructions and toward inquiry-based learning (IBL), but only now developing methods for integrating inquiry-based writing (IBW) practices into the laboratory course. Based on an earlier proposal (Science 332:919 (2011)), we designed and implemented an IBW sequence in a university bioinformatics course.

We automatically generated unique, double-blinded, biologically plausible DNA sequences for each student. After guided instruction, students investigated sequences independently and responded through IBW writing assignments. IBW assignments were structured as condensed versions of a scientific research paper, and because the sequences were double blinded, they were also assessed as authentic science and evaluated on clarity and persuasiveness.

We piloted the approach in a seven-day workshop (35 students) at Perdana University Graduate School of Medicine in Kuala Lumpur. We observed dramatically improved student engagement and indirect evidence of improved learning outcomes over a similar workshop without IBW. Based on student feedback, initial discomfort with the writing component abated in favor of an overall positive response and increasing comfort with the high demands of student writing. Similarly encouraging results were found in a semester length undergraduate module at the National University of Singapore (155 students).
Mechanical effects of MitraClip on leaflet stress and myocardial strain in functional mitral regurgitation – A finite element modeling study
Authors: Zhang Yue , Wang Vicky Y , Morgan Ashley E , Kim Jiwon , Handschumacher Mark D , Moskowitz Chaya S , Levine Robert A , Ge Liang , Guccione Julius M , Weinsaft Jonathan W , Ratcliffe Mark B
Published: July 2019

Purpose

MitraClip is the sole percutaneous device approved for functional mitral regurgitation (MR; FMR) but MR recurs in over one third of patients. As device-induced mechanical effects are a potential cause for MR recurrence, we tested the hypothesis that MitraClip increases leaflet stress and procedure-related strain in sub-valvular left ventricular (LV) myocardium in FMR associated with coronary disease (FMR-CAD).

Methods

Simulations were performed using finite element models of the LV + mitral valve based on MRI of 5 sheep with FMR-CAD. Models were modified to have a 20% increase in LV volume (↑LV_VOLUME) and MitraClip was simulated with contracting beam elements (virtual sutures) placed between nodes in the center edge of the anterior (AL) and posterior (PL) mitral leaflets. Effects of MitraClip on leaflet stress in the peri-MitraClip region of AL and PL, septo-lateral annular diameter (SLAD), and procedure-related radial strain (Err) in the sub-valvular myocardium were calculated.

Results

MitraClip increased peri-MitraClip leaflet stress at end-diastole (ED) by 22.3±7.1 kPa (p<0.0001) in AL and 14.8±1.2 kPa (p<0.0001) in PL. MitraClip decreased SLAD by 6.1±2.2 mm (p<0.0001) and increasedErrin the sub-valvular lateral LV myocardium at ED by 0.09±0.04 (p<0.0001)). Furthermore, MitraClip in ↑LV_VOLUME was associated with persistent effects at ED but also at end-systole where peri-MitraClip leaflet stress was increased in AL by 31.9±14.4 kPa (p=0.0268) and in PL by 22.5±23.7 kPa (p=0.0101).

Conclusions

MitraClip for FMR-CAD increases mitral leaflet stress and radial strain in LV sub-valvular myocardium. Mechanical effects of MitraClip are augmented by LV enlargement.
White matter hyperintensities are common in midlife and already associated with cognitive decline
Authors: d’Arbeloff Tracy , Elliott Maxwell L. , Knodt Annchen R. , Melzer Tracy R. , Keenan Ross , Ireland David , Ramrakha Sandhya , Poulton Richie , Anderson Tim , Caspi Avshalom , Moffitt Terrie E. , Hariri Ahmad R.
Published: July 2019

White matter hyperintensities (WMHs) proliferate as the brain ages and are associated with increased risk for cognitive decline as well as Alzheimer’s disease and related dementias. As such, WMHs have been targeted as a surrogate biomarker in intervention trials with older adults. However, it is unclear at what stage of aging WMHs begin to relate to cognition and if they may be a viable target for early prevention. In a population-representative birth cohort of 843 45-year-olds we measured WMHs using T2-weighted MRI, and we assessed cognitive decline from childhood to midlife. We found that WMHs were common at age 45 and that WMH volume was modestly associated with both lower childhood (ß=-0.08, p=0.013) and adult IQ (ß=-0.15, p<0.001). Moreover, WMH volume was associated with greater cognitive decline from childhood to midlife (ß=-0.09, p<0.001). Our results demonstrate that a link between WMHs and early signs of cognitive decline is detectable decades before clinical symptoms of dementia emerge. Thus, WMHs may be a useful surrogate biomarker for identifying individuals in midlife at risk for future accelerated cognitive decline and selecting participants for dementia prevention trials.
Trans- and cis-acting effects of the lncRNA Firre on epigenetic and structural features of the inactive X chromosome
Authors: Fang He , Bonora Giancarlo , Lewandowski Jordan P. , Thakur Jitendra , Filippova Galina N. , Henikoff Steven , Shendure Jay , Duan Zhijun , Rinn John L. , Deng Xinxian , Noble William S. , Disteche Christine M.
Published: July 2019

Firre encodes a lncRNA involved in nuclear organization in mammals. Here we find that Firre RNA is transcribed from the active X chromosome (Xa) and exerts trans-acting effects on the inactive X chromosome (Xi). Allelic deletion of Firre on the Xa in a mouse hybrid fibroblast cell line results in a dramatic loss of the histone modification H3K27me3 and of components of the PRC2 complex on the Xi as well as the disruption of the perinucleolar location of the Xi. These features are measurably rescued by ectopic expression of a mouse or human Firre/FIRRE cDNA transgene, strongly supporting a conserved trans-acting role of the Firre transcript in maintaining the Xi heterochromatin environment. Surprisingly, CTCF occupancy is decreased on the Xi upon loss of Firre RNA, but is partially recovered by ectopic transgene expression, suggesting a functional link between Firre RNA and CTCF in maintenance of epigenetic features and/or location of the Xi. Loss of Firre RNA results in dysregulation of genes implicated in cell division and development, but not in reactivation of genes on the Xi, which retains its bipartite structure despite some changes in chromatin contact distribution. Allelic deletion or inversion of Firre on the Xi causes localized redistribution of chromatin contacts, apparently dependent on the orientation of CTCF binding sites clustered at the locus. Thus, the Firre locus and its RNA have roles in the maintenance of epigenetic features and structure of the Xi.
Layer-by-Layer Fabrication of 3D Hydrogel Structures Using Open Microfluidics
Authors: Lee Ulri N. , Day John H. , Haack Amanda J. , Lu Wenbo , Theberge Ashleigh B. , Berthier Erwin
Published: July 2019

Patterning and 3D fabrication techniques have enabled the use of hydrogels for a number of applications including microfluidics, sensors, separations, and tissue engineering in which form fits function. Devices such as reconfigurable microvalves or implantable tissues have been created using lithography or casting techniques. Here, we present a novel open microfluidic patterning method that utilizes surface tension forces to pattern hydrogel layers on top of each other, producing 3D hydrogel structures. We use a patterning device to form a temporary open microfluidic channel on an existing gel layer, allowing the controlled flow of unpolymerized gel in regions defined by the device. Once the gel is polymerized, the patterning device can then be removed, and subsequent layers added to create a multi-layered 3D structure. The use of open-microfluidic and surface tension-based methods to define the shape of each layer enables patterning to be performed with a simple pipette, minimizing dead-volume and shear stress applied on the fluid. Our method is compatible with unmodified (native) biological hydrogels, or other non-biological materials with fluid properties compatible with capillary flow. With our open-microfluidic layer-by-layer fabrication method, we demonstrate the capability to build agarose and type I collagen structures featuring asymmetric designs, multiple components, overhanging features, and cell laden regions.
CSF sTREM2 correlates with CSF tau in advancing Parkinson’s disease
Authors: Wilson Edward N. , Swarovski Michelle S. , Linortner Patricia , Shahid Marian , Zuckerman Abigail J. , Wang Qian , Channappa Divya , Minhas Paras S. , Mhatre Siddhita D. , Plowey Edward D. , Quinn Joseph F. , Zabetian Cyrus P. , Tian Lu , Longo Frank M. , Cholerton Brenna , Montine Thomas J. , Poston Kathleen L. , Andreasson Katrin I.
Published: July 2019

Parkinson’s disease (PD) is the second most common neurodegenerative disease after Alzheimer’s disease (AD) and affects 1% of the population above 60 years old. Although PD commonly manifests with motor symptoms, a majority of patients with PD subsequently develop cognitive impairment which often progresses to dementia, a major cause of morbidity and disability. PD is characterized by α-synuclein accumulation that frequently associates with amyloid beta (Aβ) and tau fibrils, the hallmarks of AD neuropathologic changes; this co-occurrence suggests that onset of cognitive decline in PD may be associated with appearance of pathologic Aβ and/or tau. Recent studies have highlighted the appearance of the soluble form of the Triggering Receptor Expressed on Myeloid cells 2 (sTREM2) receptor in CSF during development of AD. Given the known association of microglial activation with advancing PD, we investigated whether CSF and/or plasma sTREM2 increased with progression to PD dementia. We examined 165 participants consisting of 17 cognitively normal elderly, 45 PD patients with no cognitive impairment, 86 with mild cognitive impairment, and 17 with dementia. Stratification of subjects by CSF Aβ and tau levels revealed that CSF sTREM2 concentrations were elevated in PD subgroups with abnormal tau, but not Aβ, CSF concentration. These findings indicate that CSF sTREM2 could serve as a surrogate immune biomarker of neuronal injury in PD that is associated with cognitive decline.

One sentence summary

CSF sTREM2 correlates with CSF tau in PD
Discovering functional sequences with RELICS, an analysis method for tiling CRISPR screens
Authors: Fiaux Patrick C. , Chen Hsiuyi V. , Chen Aaron R. , Chen Poshen B. , McVicker Graham
Published: July 2019

CRISPR screens are a powerful new technology for the identification of genome sequences that affect cellular phenotypes such as gene expression, survival, and proliferation. By tiling single-guide RNA (sgRNA) target sites across large genomic regions, CRISPR screens have the potential to systematically discovery novel functional sequences, however, a lack of purpose-built analysis tools limits the effectiveness of this approach. Here we describe RELICS, a Bayesian hierarchical model for the discovery of functional sequences from tiling CRISPR screens. RELICS considers the overlapping effects of multiple nearby functional sequences, accounts for the ‘area of effect’ surrounding sgRNA target sites, models overdispersion in sgRNA counts, combines information across multiple pools, and estimates the number of functional sequences supported by the data. In simulations, RELICS outperforms existing methods and provides higher resolution predictions. We apply RELICS to published CRISPR interference and CRISPR activation screens and predict novel regulatory sequences, several of which we experimentally validate. In summary, RELICS is a powerful new analysis method for tiling CRISPR screens that enables the discovery of functional sequences with unprecedented resolution and accuracy.
Power series method for solving TASEP-based models of mRNA translation
Authors: Scott S , Szavits-Nossan J
Published: July 2019

We develop a method for solving mathematical models of messenger RNA (mRNA) translation based on the totally asymmetric simple exclusion process (TASEP). Our main goal is to demonstrate that the method is versatile and applicable to realistic models of translation. To this end we consider the TASEP with codon-dependent elongation rates, premature termination due to ribosome drop-off and translation reinitiation due to circularisation of the mRNA. We apply the method to the model organism Saccharomyces cerevisiae under physiological conditions and find excellent agreements with the results of stochastic simulations. Our findings suggest that the common view on translation as being rate-limited by initiation is oversimplistic. Instead we find theoretical evidence for ribosome interference and also theoretical support for the ramp hypothesis which argues that codons at the beginning of genes have slower elongation rates in order to reduce ribosome density and jamming.
Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph
Authors: Hubisz Melissa J. , Williams Amy L. , Siepel Adam
Published: July 2019

The sequencing of Neanderthal and Denisovan genomes has yielded many new insights about interbreeding events between extinct hominins and the ancestors of modern humans. While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present an extended version of the ARGweaver algorithm, ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topology and branch lengths along the genome, but also indicate migrant lineages. The sampled ARGs can therefore be parsed to produce probabilities of introgression along the genome. We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples. We then show that the method can also detect introgressed regions stemming from older migration events, or from unsampled populations. We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. We also identify 1% of the Denisovan genome which was likely introgressed from an unsequenced hominin ancestor, and note that 15% of these regions have been passed on to modern humans through subsequent gene flow.
Fecal Microbiota Transplantation Decreases Amyloid Load and Improves Cognition in Alzheimer’s
Authors: Elangovan Shalini , Borody Thomas J , Holsinger R M Damian
Published: July 2019

The efficacy of fecal microbiota transplantation (FMT) in Alzheimer’s disease has yet to be investigated. Here, we show that FMT is capable of providing neuroprotective effects in two groups of treated 5xFAD Alzheimer’s mice, old transgenic (Tg) mice fed fecal slurry from healthy, wild-type donors of similar age (Old Tg-FO) and old mice fed fecal slurry from younger healthy, wild-type donors (Old Tg-FY). Improved spatial and recognition memory in Old Tg-FY and enhanced recognition memory in Old Tg-FO were observed when compared to Old Tg-Control mice given saline. Crucially, there was significant decreases in cortical Aβ loading in all treated mice, demonstrating the therapeutic effects of FMT in improving cognition and reducing amyloid pathology in AD brains.

One Sentence Summary

Fecal microbial transplants reduce amyloid pathology and improve cognition in Alzheimer’s mice.