Spatial metrology of dopants in silicon with exact lattice site precision

Scaling of Si-based nanoelectronics has reached the regime where device function is affected not only by the presence of individual dopants, but also by their positions in the crystal. Determination of the precise dopant location is an unsolved problem in applications from channel doping in ultrascaled transistors to quantum information processing. Here, we establish a metrology combining low-temperature scanning tunnelling microscopy (STM) imaging and a comprehensive quantum treatment of the dopant-STM system to pinpoint the exact coordinates of the dopant in the Si crystal. The technique is underpinned by the observation that STM images contain atomic-sized features in ordered patterns that are highly sensitive to the STM tip orbital and the absolute dopant lattice site. The demonstrated ability to determine the locations of P and As dopants to 5 nm depths will provide critical information for the design and optimization of nanoscale devices for classical and quantum computing applications.

Quantum simulation of the Hubbard model with dopant atoms in silicon

In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, simulation of Bose-Hubbard Hamiltonians using cold atoms revealed previously hidden local correlations. However, fermionic many-body Hubbard phenomena such as unconventional superconductivity and spin liquids are more difficult to simulate using cold atoms. To date the required single-site measurements and cooling remain problematic, while only ensemble measurements have been achieved. Here we simulate a two-site Hubbard Hamiltonian at low effective temperatures with single-site resolution using subsurface dopants in silicon. We measure quasi-particle tunnelling maps of spin-resolved states with atomic resolution, finding interference processes from which the entanglement entropy and Hubbard interactions are quantified. Entanglement, determined by spin and orbital degrees of freedom, increases with increasing valence bond length. We find separation-tunable Hubbard interaction strengths that are suitable for simulating strongly correlated phenomena in larger arrays of dopants, establishing dopants as a platform for quantum simulation of the Hubbard model.

TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins

RNA transcripts are bound and regulated by RNA-binding proteins (RBPs). Current methods for identifying in vivo targets of an RBP are imperfect and not amenable to examining small numbers of cells. To address these issues, we developed TRIBE (targets of RNA-binding proteins identified by editing), a technique that couples an RBP to the catalytic domain of the Drosophila RNA-editing enzyme ADAR and expresses the fusion protein in vivo. RBP targets are marked with novel RNA editing events and identified by sequencing RNA. We have used TRIBE to identify the targets of three RBPs (Hrp48, dFMR1, and NonA). TRIBE compares favorably to other methods, including CLIP, and we have identified RBP targets from as little as 150 specific fly neurons. TRIBE can be performed without an antibody and in small numbers of specific cells.

Depression and quality of life in hospitalised patients with congestive heart failure (CHF): A cross-sectional study from Karachi, Pakistan

Introduction

There is strong association between depression and mortality rates among patients with CHF. Despite the massive burden of cardiac disease as well as that of depression in Pakistan, there is limited data regarding the prevalence of depression in patients suffering from CHF. The aim of this study was to assess prevalence of depression in patients with CHF and to compare the health related quality of life of depressed and non-depressed patients with CHF.

Methods

A total of 1009 patients diagnosed with CHF were recruited from different public hospitals in Karachi, Pakistan. Depression was assessed at baseline using the Beck Depression Inventory (BDI) and health related quality of life was assessed using Euro Qol (EQ-5D).

Results

Of the 1009 participants recruited to the study, 66.4% (n = 670) met the threshold for depression using the BDI measure. Of the depressed patients, 66.7% (n = 447) were male. Preliminary results indicate that participants who were depressed at baseline had poorer health related quality of life on EQ-5D measures as compared to those who were non-depressed (mean EQ-5D descriptive score 10.45 in depressed patients vs 7.37 in non-depressed patients and mean EQ-5D visual scale score 35.09 in depressed patients vs 52.19 in non-depressed patients).

Conclusion

Considering the high prevalence of depression and its serious negative impact on quality of life of patients suffering from chronic physical illness, it is important to design and test culturally adapted psychosocial interventions to reduce depression and improve quality of life for these patients.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals

The Piwi pathway is deeply conserved amongst animals because one of its essential functions is to repress transposons. However, many Piwi-interacting RNAs (piRNAs) do not base-pair to transposons and remain mysterious in their targeting function. The sheer number of piRNA cluster (piC) loci in animal genomes and infrequent piRNA sequence conservation also present challenges in determining which piC loci are most important for development. To address this question, we determined the piRNA expression patterns of piC loci across a wide phylogenetic spectrum of animals, and reveal that most genic and intergenic piC loci evolve rapidly in their capacity to generate piRNAs, regardless of known transposon silencing function. Surprisingly, we also uncovered a distinct set of piC loci with piRNA expression conserved deeply in Eutherian mammals. We name these loci Eutherian-Conserved piRNA cluster (ECpiC) loci. Supporting the hypothesis that conservation of piRNA expression across ~100 million years of Eutherian evolution implies function, we determined that one ECpiC locus generates abundant piRNAs antisense to the STOX1 transcript, a gene clinically associated with preeclampsia. Furthermore, we confirmed reduced piRNAs in existing mouse mutations at ECpiC-Asb1 and -Cbl, which also display spermatogenic defects. The Asb1 mutant testes with strongly reduced Asb1 piRNAs also exhibit up-regulated gene expression profiles. These data indicate ECpiC loci may be specially adapted to support Eutherian reproduction.

Animal genomes from flies to humans contain many hundreds of non-coding elements called Piwi-interacting RNAs (piRNAs) cluster loci (piC loci). Some of these elements generate piRNAs that direct the silencing of transposable elements, which are pervasive genetic parasites. However, we lack an understanding of the targeting function for the remaining bulk of piRNAs because their loci are not complementarity to transposable elements. In addition, the field does not know if all piC loci are quickly evolving, or if some piC loci might be deeply conserved in piRNA expression, an indication of its potentially functional importance. Our study confirms the highly rapid evolution in piRNA expression capacity for the majority of piC loci in flies and mammals, with many clade- and species-specific piC loci expression patterns. In spite of this, we also discover a cohort of piC loci that are deeply conserved in piRNA expression from the human to the dog, a significantly broad phylogenetic spectrum of eutherian mammals. However, this conservation in piRNA expression ends at non-eutherian mammals like marsupials and monotremes. Existing mutations in two of these Eutherian-Conserved piC (ECpiC) loci impair mouse reproduction and abrogate piRNA production. Therefore, we suggest these ECpiC loci are conserved for piRNA expression due to their important function in eutherian reproduction and stand out as prime candidates for future genetic studies.

Unique transposon landscapes are pervasive across Drosophila melanogaster genomes

To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of >300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, >500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (<25%) of transposon families comprise the majority (>70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.

Ambras Syndrome: First Reported Case in Bangladesh and its Oral Rehabilitation

People with rare hypertrichosis syndromes became crowd-drawing money-making phenomena in many 19th century sideshow acts. These individuals have been referred to as dog-men, hair-men, and werewolves. In 1993, Baumister et al. described congenital hypertrichosis lanuginose or Ambras syndrome: a distinct form of congenital hypertrichosis characterized by excessive hair growth over the body and face associated with facial and occasional dental anomalies. Much is not known about this syndrome since fewer than 50 cases have been documented worldwide. In this case report, a nine year old girl presented with excessive hair growth throughout her body that was denser along her midline. Furthermore, her face displayed the typical dysmorphic features characteristic of Ambras syndrome: a round tip nose, thickened nasal cartilage, antiverted nares, prominent philtrum with deep groove, and a trapezoid mouth. Oral examination revealed normal oral mucosa with completely missing and unerupted decidious and permanent teeth. Panoramic radiographs confirmed unerupted deciduous teeth. Previous case reports have mentioned the presence of occasional dental anomalies such as retarded first and second dentition and absence of some teeth. However, this is the first reported case of Ambras syndrome presenting with complete anodontia. Prior cytogenetic studies performed on persons with Ambras syndrome have implicated a balanced pericentric inversion of chromosome 8. However, it is likely that dental anomalies are likely a result of a different genetic rearrangement. Further studies are needed to explore the cause of this rare phenotype of Ambras syndrome with complete unerupted dentition.

Study on Association of Maternal Serum Triglyceride with Pre-eclampsia

Till now pre-eclampsia is a disease of multiple theories. This case control study was carried out in the department of Obstetrics and Gynaecology of Bangabandhu Sheikh Mujib Medical University Hospital and Dhaka Medical College Hospital, from January 2006 to December 2007 to determine the association of maternal serum triglyceride with pre-eclampsia. Ninety pregnant women were studied, among them 45 patients were pre-eclamptic and served as case and 45 normal healthy pregnant women served as control. Estimation of serum triglyceride levels of all study patients was done with the help of enzymatic method. The mean (± SD) systolic blood pressure was 152.4 ± 19.8 mmHg in study group and 112.0 ± 8.9 mmHg in control group (p<0.05). Similarly the mean (± SD) diastolic blood pressure was 103.1 ± 12.2 mmHg in case group and 75.5 ± 6.6 mmHg in control group (p<0.05). Serum triglyceride level was more than the normal reference value in pre-eclamptic group. The mean (± SD) serum triglyceride level was 242.9 ± 36.8 mg/dl in case group and 184.6 ± 12.5mg/dl in control group. Statistically the difference was significant (p<0.05). The level of serum triglyceride positively correlated with the rise of blood pressure and degree of albuminuria. Thus serum triglyceride level increase in pre-eclampsia and the level correlate with the severity of the disease.

Spatially resolved resonant tunneling on single atoms in silicon

The ability to control single dopants in solid-state devices has opened the way towards reliable quantum computation schemes. In this perspective it is essential to understand the impact of interfaces and electric fields, inherent to address coherent electronic manipulation, on the dopants atomic scale properties. This requires both fine energetic and spatial resolution of the energy spectrum and wave-function, respectively. Here we present an experiment fulfilling both conditions: we perform transport on single donors in silicon close to a vacuum interface using a scanning tunneling microscope (STM) in the single electron tunneling regime. The spatial degrees of freedom of the STM tip provide a versatility allowing a unique understanding of electrostatics. We obtain the absolute energy scale from the thermal broadening of the resonant peaks, allowing us to deduce the charging energies of the donors. Finally we use a rate equations model to derive the current in presence of an excited state, highlighting the benefits of the highly tunable vacuum tunnel rates which should be exploited in further experiments. This work provides a general framework to investigate dopant-based systems at the atomic scale.

Role of D-dimer in determining coagulability status in pre-eclamptic and normotensive pregnant women

A cross sectional study was carried out from January 2007 to December 2008 in the department of Obstetrics and Gynaecology, Dhaka Medical College Hospital, Dhaka in collaboration with Department of Haematology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh. Pregnant women with pre-eclampsia attending at Out-patient Department (OPD) and admitted in In-patient Department of Obstetrics and Gynaecology Dhaka Medical College Hospital, Dhaka were selected as cases. Healthy and uncomplicated pregnant women admitted in the same hospital were taken as controls. The study showed that 26-30 years and 21-25 years age category was higher in the case and control groups and the mean age was significantly higher in case group compared to control group (p=0.025). The study showed that 44% of case group had a significantly high level of plasma D-dimer (>0.5μg/ml) as opposed to control group (8%) (p<0.001). Estimation of odds ratio demonstrates that pre-eclamptic women (case) had 9 times (95% of CI = 2.8 - 28.9) more risk of having plasma D-dimer >0.5μg/ml than that of normal pregnant women (control). The mean systolic and diastolic blood pressures in patients with plasma D-dimer >0.5μg/ml were considerably higher than those who had plasma D-dimer ≤0.5μg/ml (p<0.001). The study showed that majority (81.8%) of pre-eclamptic women with plasma D-dimer >0.5μg/ml had systolic blood pressure ≥ 160 mm Hg compared to 46.4% of those who had plasma D-dimer ≤0.5μg/ml (p=0.010). And ninety percent of pre-eclamptic women with plasma D-dimer >0.5μg/ml had exhibited severe proteinuria as opposed to 53.6% of those who had plasma D-dimer ≤0.5μg/ml (p=0.017). The study concludes that plasma D-dimer level can easily be used in screening for the hypercoagulable state in pre-eclamptic patients which have preventive and therapeutic implications.

Policy advocacy and leadership training for formerly incarcerated women: an empowerment evaluation of ReConnect, a program of the Women in Prison Project, Correctional Association of New York

There is limited knowledge on re-entry initiatives for formerly incarcerated women specifically on building women's advocacy and leadership skills. Our research highlights an empowerment evaluation on ReConnect, a 12-session; innovative advocacy and leadership development program rooted in an integrated framework of empowerment, and transformational leadership theories. Using thematic analysis, we coded three focus groups with 24 graduates, for themes that matched our framework's concepts. ReConnect graduates reported being empowered by the information they received on parental rights, housing, and employment. Participants agreed that ReConnect improved their communication skills, preparing them to advocate for themselves and community members.

Surgical delivery of drug releasing poly(lactic-co-glycolic acid)/poly(ethylene glycol) paste with in vivo effects against glioblastoma

INTRODUCTION

The median survival of patients with glioblastoma multiforme (astrocytoma grade 4) remains less than 18 months despite radical surgery, radiotherapy and systemic chemotherapy. Surgical implantation of chemotherapy eluting wafers into the resection cavity has been shown to improve length of survival but the current licensed therapy has several drawbacks. This paper investigates in vivo efficacy of a novel drug eluting paste in glioblastoma.

METHODS

Poly(lactic-co-glycolic acid)/poly(ethylene glycol) (PLGA/PEG) self-sintering paste was loaded with the chemotherapeutic agent etoposide and delivered surgically into partially resected tumours in a flank murine glioblastoma xenograft model.

RESULTS

Surgical delivery of the paste was successful and practical, with no toxicity or surgical morbidity to the animals. The paste was retained in the tumour cavity, and preliminary results suggest a useful antitumour and antiangiogenic effect, particularly at higher doses. Bioluminescent imaging was not affected significantly by the presence of the paste in the tumour.

CONCLUSIONS

Chemotherapy loaded PLGA/PEG paste seems to be a promising technology capable of delivering active drugs into partially resected tumours. The preliminary results of this study suggest efficacy with no toxicity and will lead to larger scale efficacy studies in orthotopic glioblastoma models.

Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures

Piwi proteins and Piwi-interacting RNAs (piRNAs) repress transposable elements (TEs) from mobilizing in gonadal cells. To determine the spectrum of piRNA-regulated targets that may extend beyond TEs, we conducted a genome-wide survey for transcripts associated with PIWI and for transcripts affected by PIWI knockdown in Drosophila ovarian somatic sheet (OSS) cells, a follicle cell line expressing the Piwi pathway. Despite the immense sequence diversity among OSS cell piRNAs, our analysis indicates that TE transcripts are the major transcripts associated with and directly regulated by PIWI. However, several coding genes were indirectly regulated by PIWI via an adjacent de novo TE insertion that generated a nascent TE transcript. Interestingly, we noticed that PIWI-regulated genes in OSS cells greatly differed from genes affected in a related follicle cell culture, ovarian somatic cells (OSCs). Therefore, we characterized the distinct genomic TE insertions across four OSS and OSC lines and discovered dynamic TE landscapes in gonadal cultures that were defined by a subset of active TEs. Particular de novo TEs appeared to stimulate the expression of novel candidate long noncoding RNAs (lncRNAs) in a cell lineage-specific manner, and some of these TE-associated lncRNAs were associated with PIWI and overlapped PIWI-regulated genes. Our analyses of OSCs and OSS cells demonstrate that despite having a Piwi pathway to suppress endogenous mobile elements, gonadal cell TE landscapes can still dramatically change and create transcriptome diversity.

Spatially resolving valley quantum interference of a donor in silicon

Electron and nuclear spins of donor ensembles in isotopically pure silicon experience a vacuum-like environment, giving them extraordinary coherence. However, in contrast to a real vacuum, electrons in silicon occupy quantum superpositions of valleys in momentum space. Addressable single-qubit and two-qubit operations in silicon require that qubits are placed near interfaces, modifying the valley degrees of freedom associated with these quantum superpositions and strongly influencing qubit relaxation and exchange processes. Yet to date, spectroscopic measurements have only probed wavefunctions indirectly, preventing direct experimental access to valley population, donor position and environment. Here we directly probe the probability density of single quantum states of individual subsurface donors, in real space and reciprocal space, using scanning tunnelling spectroscopy. We directly observe quantum mechanical valley interference patterns associated with linear superpositions of valleys in the donor ground state. The valley population is found to be within 5% of a bulk donor when 2.85 ± 0.45 nm from the interface, indicating that valley-perturbation-induced enhancement of spin relaxation will be negligible for depths greater than 3 nm. The observed valley interference will render two-qubit exchange gates sensitive to atomic-scale variations in positions of subsurface donors. Moreover, these results will also be of interest for emerging schemes proposing to encode information directly in valley polarization.

Pregnancy with myasthenia gravis

Myasthenia gravis (MG) is an autoimmune disorder of the neuromuscular transmission, caused by auto antibodies against the nicotinic acetylcholine receptor. These antibodies of the IgG isotype are detected in 80-90% of generalized MG and in 50-70% of ocular MG. Seronegative MG is caused by humoral factors. Prevalence of MG lies between 1 in 10.000 and 1 in 50.000, with 2/3 of affected individuals being female. In the case of maternal myasthenia gravis, both the mother and the child may develop myasthenia symptoms with varying degrees of weakness and progressive fatigability of the skeletal muscles. Data for the case report were generated by reviewing labour, delivery, and postpartal records. We present a 26 years old lady who suffered from a generalized form of myasthenia gravis since the age of 15. She got herself admitted to a neurologic clinic for a myasthenic crisis when she was two and half months pregnant. The patient was treated with anticholinesterase medication, corticosteroids and intravenous immunoglobulin. Clinically, the patient's condition improved significantly during pregnancy. Delivery and the post delivery period were also normal for the patient. Myasthenia gravis especially when associated with pregnancy is a high-risk disease. As this disease predominantly occurs in women of reproductive age, it is important to be aware of this condition in obstetrics and its interdisciplinary diagnostic and therapeutic management is required.

Early surgery for epiretinal membrane preserves more vision for patients

PURPOSE

To establish whether early vitrectomy for epiretinal membrane (ERM) is preferable to delayed surgery.

METHODS

We carried out a retrospective study of 120 eyes from 120 patients with pre-operative visual acuity (VA) of 6/60 or better. Pre-operative logMAR score was considered to act as an appropriate proxy measure for time of surgical procedure, with scores of 0.3 or less considered to represent early surgery, scores of 0.4 or 0.5 considered to represent medium surgery, and scores of 0.6 or more considered to represent late surgery for ERM. Patients were either pseudophakic at the time of vitrectomy or underwent combined phaco-vitrectomy for symptomatic ERM.

RESULTS

Evaluation of parameter coefficients indicated that controlling for other factors, a delay of the surgical procedure from a state of early to medium corresponded to an increase (ie, disbenefit) of 0.074 units in post-operative logMAR score (95% confidence interval -0.001-0.15). A delay of the surgical procedure from a state of early to late corresponded to an increase (ie, disbenefit) of 0.21 units in post-operative logMAR score (95% confidence interval 0.13-0.29). Mean post-operative VA for early surgery was 0.16, out of which 36.2% of patients had a LogMAR score of 0.1 or better. This is in comparison to 17.2% in late ERM (those with a pre-operative logMAR score of 0.6 or more).

CONCLUSION

We conclude that early surgery is associated with a lower (ie, better) post-operative logMAR score. Vitrectomy for early symptomatic ERM, in carefully selected patients, is beneficial in preserving excellent vision and allows quicker visual rehabilitation.