Scalable 3D Reconstruction From Single Particle X-Ray Diffraction Images Based on Online Machine Learning

X-ray free-electron lasers (XFELs) offer unique capabilities for measuring the structure and dynamics of biomolecules, helping us understand the basic building blocks of life. Notably, high-repetition-rate XFELs enable single particle imaging (X-ray SPI) where individual, weakly scattering biomolecules are imaged under near-physiological conditions with the opportunity to access fleeting states that cannot be captured in cryogenic or crystallized conditions. Existing X-ray SPI reconstruction algorithms, which estimate the unknown orientation of a particle in each captured image as well as its shared 3D structure, are inadequate in handling the massive datasets generated by these emerging XFELs. Here, we introduce X-RAI, an online reconstruction framework that estimates the structure of a 3D macromolecule from large X-ray SPI datasets. X-RAI consists of a convolutional encoder, which amortizes pose estimation over large datasets, as well as a physics-based decoder, which employs an implicit neural representation to enable high-quality 3D reconstruction in an end-to-end, self-supervised manner. We demonstrate that X-RAI achieves state-of-the-art performance for small-scale datasets in simulation and challenging experimental settings and demonstrate its unprecedented ability to process large datasets containing millions of diffraction images in an online fashion. These abilities signify a paradigm shift in X-ray SPI towards real-time capture and reconstruction.

Impact of changing indications and increased utilization of fetal echocardiography on prenatal detection of congenital heart disease

BACKGROUND

Antenatal diagnosis of congenital heart defects (CHD) can impact outcomes in neonates with severe CHD. Obstetric screening guidelines and the indications for fetal echocardiography (FE) have evolved in an attempt to improve the early prenatal detection of CHD. Analyzing yield for specific indications will help clinicians better stratify at-risk pregnancies.

METHODS

Retrospective cohort study of all FE performed between 2000 and 2010 at a single tertiary care academic medical center in New York City. A total of 9878 FE met inclusion criteria for our study. In cases of multiple gestations (MG), each fetus was counted as a separate study.

RESULTS

The number of new diagnosis of fetal CHD by FEs increased 200%. There was a statistically significant increase in those referred for suspected CHD, increased nuchal translucency (NT), MG, and suboptimal imaging (P < .001). The indication of "suboptimal imaging" (SO) not only accounted for 5.23% of all referrals from 2000 to 2002, compared to 22.26% of all referrals from 2008 to 2010 (P < .0001), but also had the lowest yield for diagnoses of CHD (P < .02).

CONCLUSIONS

Over the past decade, there has been an increase in utilization of FE with a proportional increase in prenatally diagnosed CHD. For indications such as suspected CHD, NT and MG increases in referrals have led to a proportionate increase in fetal diagnosis of CHD. SO as an indication has the lowest yield of fetal diagnosis of CHD. Antenatal detection of CHD may be improved by a change in obstetric imaging protocols to ensure appropriate referrals.

EVALUATION OF MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION AS A TOOL FOR DIAGNOSIS AND CARRIER DETECTION IN FAMILIES WITH A DYSTROPHINOPATHY

We set out to evaluate multiplex ligation dependent probe amplification (MLPA) as a tool for diagnosis and carrier detection in families with a dystrophinopathy. Fifty three Indian families with provisional diagnosis of Duchene muscular dystrophy or Becker muscular dystrophy were evaluated by MLPA and multiplex polymerase chain reaction (PCR). Sanger sequencing was used to analyze the entire gene in one patient. Mothers were tested for carrier status whenever possible. Molecular analysis of DMD gene by combining MLPA and multiplex PCR yielded a mutation detection rate of 62% (33/53). Deletions were detected in 27/53 (51%) cases, duplications in 5/53 (9%) cases, a small deletion one case and Sanger sequencing detected a nonsense mutation in one case. Mutation was not detected in 36% (19/53) cases. Fifty six percent of mothers (9/16) were found to be carriers. MLPA helped to refine the results of multiplex PCR testing in 22 patients (5 duplications, 16 deletions and one small deletion). We also describe a situation where a deletion of single exon on MLPA (but not detected by multiplex PCR) was actually due to a deletion of two nucleotides in the probe ligation site. MLPA appears to score over multiplex PCR in diagnosis and carrier detection, specifically by detecting deletions and duplications that are not detected by traditional multiplex PCR.

Factors associated with acute diarrhoea in children in Dhahira, Oman: a hospital-based study

To elucidate the bacterial etiology of childhood diarrhoea in Dhahira, 856 children < 12 years admitted for diarrhoea to Ibri Regional Referral Hospital from 2000 to 2002 were studied. The mean age was 2.4 (SD 2.3) years; the majority (92.9%) were < 5 years. Bacterial etiology was found in 15.2% of cases; 10.6% due to Shigella and 2.1% to Salmonella. Sh. sonnei was the commonest Shigella serogroup isolated. Salmonella infection was significantly associated with cramps, while Shigella infection was associated with fever, bloody stools and cramps. Antibiotics were prescribed in 36.2% of cases and the resistance to the common antibiotics tested was low.

Psychological disturbance among 5- to 8-year-old school children: a study from India

This paper presents findings on the prevalence of psychological disturbance among a sample of 5- to 8-year-old Indian school children. The study was cross-sectional with a two-instrument, two-phase design. In the first phase (screening), 48 teachers rated 1535 children (810 boys and 725 girls) drawn from five schools in Bangalore city on the 26-item Children's Behaviour Questionnaire (CBQ). This resulted in 281 children being identified as disturbed, giving a prevalence of 18.3%. In the second phase, 279 of the children identified as disturbed on the CBQ and a matched group of 272 'non-disturbed children' (182 boys and 90 girls) were again rated by teachers, this time using the Child Behaviour Checklist--Teacher Report Form, yielding a corrected prevalence rate of 19.8%. In the same phase, 166 of the disturbed children and a matched group of 169 non-disturbed children were rated by parents using the Child Behaviour Checklist, yielding a corrected prevalence rate of 31.7%. A larger proportion of boys than girls were identified as disturbed by teachers, whereas parents identified a large proportion of disturbed girls. Boys were found to manifest externalizing problems more often, while girls more frequently showed internalizing problems. Learning problems were identified in a substantial number of disturbed boys and girls.

Prevalence of scholastic backwardness among five to eight year old children

The present paper reports the findings of a study of scholastic backwardness among five to eight year old school going children. 1535 children were screened by their class teachers, of which 10.23% were found to have scholastic backwardness. No gender differences were noticed. The rates of specific difficulties such as reading, writing and arithmetic were found to be 4.69%, 5.15% and 15.96% respectively. About 26% of the scholastically backward children were also found to have psychological disturbance. In addition, they most often came from families which could not afford basic amenities, had fathers with alcohol dependence, inconsistent disciplining and poor parental interaction. They also had more frequent school changes, tution attendence and fewer hobbies compared to the scholastically superior children.

Family pathology and anorexia in the Indian context

Frequent associations have been found between family interaction and anorectic behaviour. Family theorists have viewed anorexia as a manifestation of a dysfunctional family system. We report three families of cases of anorexia (one male and two female) where the symptom was a reflection of family pathology and was being maintained by it. The cases emphasize the need to assess families of anorectics in detail and view them in the cultural context of eating.