An AI-based approach driven by genotypes and phenotypes to uplift the diagnostic yield of genetic diseases.

Identifying disease-causing variants in Rare Disease patients' genome is a challenging problem. To accomplish this task, we describe a machine learning framework, that we called "Suggested Diagnosis", whose aim is to prioritize genetic variants in an exome/genome based on the probability of being disease-causing. To do so, our method leverages standard guidelines for germline variant interpretation as defined by the American College of Human Genomics (ACMG) and the Association for Molecular Pathology (AMP), inheritance information, phenotypic similarity, and variant quality. Starting from (1) the VCF file containing proband's variants, (2) the list of proband's phenotypes encoded in Human Phenotype Ontology terms, and optionally (3) the information about family members (if available), the "Suggested Diagnosis" ranks all the variants according to their machine learning prediction. This method significantly reduces the number of variants that need to be evaluated by geneticists by pinpointing causative variants in the very first positions of the prioritized list. Most importantly, our approach proved to be among the top performers within the CAGI6 Rare Genome Project Challenge, where it was able to rank the true causative variant among the first positions and, uniquely among all the challenge participants, increased the diagnostic yield of 12.5% by solving 2 undiagnosed cases.

Breast Edema after Conservative Surgery for Early-Stage Breast Cancer: A Retrospective Single-Center Assessment of Risk Factors.

Breast-conserving surgery (BCS) is the standard of care for early-stage breast cancer. We retrospectively enrolled 530 patients (mean age: 62.96 ± 12.69 years) undergoing BCS between January 1, 2018, and December 31, 2019. During the COVID-19 pandemic, all patients with at least 1 year of follow-up were telephonically asked after surgery to provide clinical signs and symptoms attributable to postoperative breast cancer-related lymphedema of the breast (BCRL-B). Thirty-one (5.8%) patients reported breast edema and were visited to measure the tissue dielectric constant (TDC) and to assess the induration of the skin. There was a difference seen in treatment with lumpectomy + ALND performed more frequently in patients with (29%) than without (12%) BCRL-B. In the subgroup of patients with BCRL-B (n=31), significantly higher values of local total water were calculated in the nine patients who underwent Lump + ALND procedure (1.86 ± 0.48 vs. 1.48 ± 0.38; p = 0.046). Among patients with BCRL-B (n=31), in eight patients (25.8%) tissue induration measured with SkinFibroMeter was >0.100 N, thus suggesting tissue fibrosis. Cumulative survival probability at 1-year after surgery was 0.992. No statistical differences in 1-year survival after surgery were found for type of surgery (p = 0.890) or absence/presence of BCRL-B (p = 0.480). In univariate logistic regression, only lumpectomy + ALND surgery (p = 0.009) and any subsequent axillary lymph node removal surgery (p = 0.003) were associated with BCRL-B. Both of these variables were also found to be statistically significant in the multivariate regression model. Further prospective research is warranted to analyze potentential predictors of BCRL-B and to reduce/ prevent this complication.

Impact of blood flow-restricted bodyweight exercise on skeletal muscle adaptations.

This study ascertains the ability of bodyweight blood flow-restricted (BFR) exercise training to promote skeletal muscle adaptations of significance for muscle accretion and metabolism. Six healthy young individuals (three males and three females) performed six weeks of bodyweight BFR training. Each session consisted of five sets of sit-to-stand BFR exercise to volitional failure with 30-second inter-set recovery. Prior to, and at least 72 h after training, muscle biopsies were taken from m. vastus lateralis to assess changes in fibre type-specific cross-sectional area (CSA), satellite cell (SC) and myonuclei content and capillarization, as well as mitochondrial protein expression. Furthermore, magnetic resonance imaging was used to assess changes in whole thigh muscle CSA. Finally, isometric knee extensor muscle strength was evaluated. An increase in knee extensor whole muscle CSA was observed at middle and distal localizations after training (3·2% and 3·5%, respectively) (P<0·05), and a trend was observed towards an increase in type I fibre CSA, whereas muscle strength did not increase. Additionally, the number of SCs and myonuclei associated with type I fibres increased by 65·7% and 20%, respectively (P<0·05). No significant changes were observed in measures of muscle capillarization and mitochondrial proteins. In conclusion, six weeks of bodyweight-based BFR exercise promoted myocellular adaptations related to muscle accretion, but not metabolic properties. Moreover, the study revealed that an appropriate total training volume needs further investigation before recommending bodyweight BFR to patient populations.

Associated decrements in rate of force development and neural drive after maximal eccentric exercise.

The present study investigated the changes in contractile rate of force development (RFD) and the neural drive following a single bout of eccentric exercise. Twenty-four subjects performed 15 × 10 maximal isokinetic eccentric knee extensor contractions. Prior to and at 24, 48, 72, 96, and 168 h during post-exercise recovery, isometric RFD (30, 50 100, and 200 ms), normalized RFD [1/6,1/2, and 2/3 of maximal voluntary contraction (MVC)] and rate of electromyography rise (RER; 30, 50, and 75 ms) were measured. RFD decreased by 28-42% peaking at 48 h (P < 0.01-P < 0.001) and remained depressed at 168 h (P < 0.05). Normalized RFD at 2/3 of MVC decreased by 22-39% (P < 0.01), peaked at 72 h and returned to baseline at 168 h. These changes in RFD were associated with a decrease in RER at 48 h-96 h (P < 0.05-P < 0.001). Accumulated changes (area under curve) revealed a greater relative decrease in accumulated RFD at 100 ms by -2727 ± 309 (%h; P < 0.05) and 200 ms by -3035 ± 271 (%h; P < 0.001) compared with MVC, which decreased, by -1956 ± 234 (%h). In conclusion, RFD and RER are both markedly reduced following a bout of maximal eccentric exercise. This association suggests that exercise-induced decrements in RFD can, in part, be explained decrements in neural drive.

The neuron-derived orphan receptor 1 (NOR1) is induced upon human alternative macrophage polarization and stimulates the expression of markers of the M2 phenotype.

BACKGROUND: Atherosclerosis is an inflammatory disease in which macrophages play a crucial role. Macrophages are present in different phenotypes, with at the extremes of the spectrum the classical M1 pro-inflammatory and the alternative M2 anti-inflammatory macrophages. The neuron-derived orphan receptor 1 (NOR1), together with Nur77 and Nurr1, are members of the NR4A orphan nuclear receptor family, expressed in human atherosclerotic lesion macrophages. However, the role of NOR1 in human macrophages has not been studied yet. OBJECTIVES: To determine the expression and the functions of NOR1 in human alternative macrophages. METHODS AND RESULTS: In vitro IL-4 polarization of primary monocytes into alternative M2 macrophages enhances NOR1 expression in human but not in mouse macrophages. Moreover, NOR1 expression is most abundant in CD68+MR+ alternative macrophage-enriched areas of human atherosclerotic plaques in vivo. Silencing NOR1 in human alternative macrophages decreases the expression of several M2 markers such as the Mannose Receptor (MR), Interleukin-1 Receptor antagonist (IL-1Ra), CD200 Receptor (CD200R), coagulation factor XIII A1 polypeptide (F13A1), Interleukin 10 (IL-10) and the Peroxisome Proliferator-Activated Receptor (PPAR)γ. Bioinformatical analysis identified F13A1, IL-1Ra, IL-10 and the Matrix Metalloproteinase-9 (MMP9) as potential target genes of NOR1 in human alternative macrophages. Moreover, expression and enzymatic activity of MMP9 are induced by silencing and repressed by NOR1 overexpression in M2 macrophages. CONCLUSIONS: These data identify NOR1 as a transcription factor induced during alternative differentiation of human macrophages and demonstrate that NOR1 modifies the alternative macrophage phenotype.

Blood flow restricted and traditional resistance training performed to fatigue produce equal muscle hypertrophy.

This study investigated the hypertrophic potential of load-matched blood-flow restricted resistance training (BFR) vs free-flow traditional resistance training (low-load TRT) performed to fatigue. Ten healthy young subjects performed unilateral BFR and contralateral low-load TRT elbow flexor dumbbell curl with 40% of one repetition maximum until volitional concentric failure 3 days per week for 6 weeks. Prior to and at 3 (post-3) and 10 (post-10) days post-training, magnetic resonance imaging (MRI) was used to estimate elbow flexor muscle volume and muscle water content accumulation through training. Acute changes in muscle thickness following an early vs a late exercise bout were measured with ultrasound to determine muscle swelling during the immediate 0-48 h post-exercise. Total work was threefold lower for BFR compared with low-load TRT (P < 0.001). Both BRF and low-load TRT increased muscle volume by approximately 12% at post-3 and post-10 (P < 0.01) with no changes in MRI-determined water content. Training increased muscle thickness during the immediate 48 h post-exercise (P < 0.001) and to greater extent with BRF (P < 0.05) in the early training phase. In conclusion, BFR and low-load TRT, when performed to fatigue, produce equal muscle hypertrophy, which may partly rely on transient exercise-induced increases in muscle water content.

Utilization of by-products from ethanol production as substrate for biogas production.

The aims of this work were to determine the specific biogas yields of steam-exploded sugarcane straw and bagasse as well as to estimate their energy potential under Brazilian conditions. Steam-explosion was carried out under different time and temperature conditions. The specific biogas yields were analyzed in batch-tests according to VDI 4630. Results have shown that steam-explosion pre-treatment increased the specific biogas yields of straw and bagasse significantly compared to the untreated material. The utilization of these by-products can contribute to 5% of the total energy consumption and thereby higher energy independence in Brazil. Further efforts in defining the optimum pretreatment conditions with steam-explosion as well as implementing this technology in large scale plants should be made.

Schwannoma of thyroid bed. A case report and considerations on interdisciplinary collaboration.

Schwannoma of the thyroid bed is extremely rare, but is known to simulate a thyroid nodule. A retrospective review is reported of a 64-year-old female patient with a thyroid nodule who had been submitted to pre-operative fine-needle aspiration biopsy, judged inadequate, following which total thyroidectomy was performed. On histological examination, the nodule (in the thyroid bed) was found to be a schwannoma. This case report stresses the importance of interdisciplinary collaboration. Better co-operation between surgeon, pathologist and radiologist may have led to correct pre-operative diagnosis with sparing of at least half the thyroid.

Protective effects of lactic acid on force production in rat skeletal muscle.

1. During strenuous exercise lactic acid accumulates producing a reduction in muscle pH. In addition, exercise causes a loss of muscle K(+) leading to an increased concentration of extracellular K(+) ([K(+)](o)). Individually, reduced pH and increased [K(+)](o) have both been suggested to contribute to muscle fatigue. 2. To study the combined effect of these changes on muscle function, isolated rat soleus muscles were incubated at a [K(+)](o) of 11 mM, which reduced tetanic force by 75 %. Subsequent addition of 20 mM lactic acid led, however, to an almost complete force recovery. A similar recovery was observed if pH was reduced by adding propionic acid or increasing the CO(2) tension. 3. The recovery of force was associated with a recovery of muscle excitability as assessed from compound action potentials. In contrast, acidification had no effect on the membrane potential or the Ca(2+) handling of the muscles. 4. It is concluded that acidification counteracts the depressing effects of elevated [K(+)](o) on muscle excitability and force. Since intense exercise is associated with increased [K(+)](o), this indicates that, in contrast to the often suggested role for acidosis as a cause of muscle fatigue, acidosis may protect against fatigue. Moreover, it suggests that elevated [K(+)](o) is of less importance for fatigue than indicated by previous studies on isolated muscles.

Distant metastases from nasopharyngeal cancer.

Undifferentiated carcinoma is the most frequent nasopharyngeal cancer; it has a typical pathognomonic histological pattern, a close relationship to Epstein-Barr virus (EBV), a peculiar natural history and a good prognosis. It has an early tendency to locally spread to the parapharyngeal space. Nodal involvement is highly frequent (70-90%) and bulky regardless of the size of the primary. Literature reports up to 11% distant metastases at presentation and up to 87% at autoptic studies. Pretreatment work-up should include: personal history, clinical and fiberscopic examination, magnetic resonance imaging (MRI) or computed tomography (CT) scan of the base of the skull and neck, histology of the primary and cytology of neck lumps, bone marrow aspiration and biopsy, and EBV serological profile. Clinical and pathological factors predicting possible distant spread are primary tumor and node extension, and treatment failure. Up to now no reliable predictive biological markers have been identified. After treatment, distant metastases are found in about 30% of patients within 5 years and generally have a bad prognosis. Metastatic nodes above the clavicle, in absence of locoregional failure, aggressively treated with chemoradiotherapy, have a disease-free survival longer than 5 years. The following is the suggested posttreatment work-up for early diagnosis of these salvageable patients: clinical and fiberscopic evaluation every 3 months for 2 years and later on every 6 months; skull base and neck MRI or CT scan, and chest CT scan at 6, 12, 18, 24, 36, 48 and 60 months; EBV serological evaluation.

Stapes surgery and psychiatric complications.

Changes in auditory perception can cause disturbances in development and personality. This phenomenon has been studied in particular in children hearing loss or in progressive or sudden hearing loss in the adult. We present the case of a patient with psychobehavioural alterations after restoration of hearing following a small fenestra stapedectomy for bilateral otosclerosis with moderate-severe hearing impairment. The diagnosis, physiopathology and medicolegal implications are discussed.

[Modification in some nasal function parameters after metacholine stimulation and pretreatment with ipratropium bromide]. / Modificazioni di alcuni parametri di funzionalità nasale dopo stimolazione con metacolina e pretrattamento con ipratropio bromuro.

Experimental research conducted on normal subjects and on perennial rhinitis sufferers demonstrates that the application of metacholine stimulates nasal secretions and that this effect is inhibited by pretreatment with ipratropium bromide. Using the Baroody et al. method, a group of 20 healthy volunteers was used to check the effect metacholine and ipratropium/metacholine had on nasal secretions. At the same time a study was performed to determine whether these treatments modify other nasal functions: turbinate blood flow, nasal resistance, mucociliar transport. The data confirm earlier observations regarding the effect of metacholine and ipratropium on nasal secretions. A parallel effect is also seen in mucociliary transport time, most likely linked to modifications in the rheological characteristics of the mucous. On the other hand, no significant difference was found in the other functions studied: turbinate blood flow and nasal resistance. We can consider metacholine and ipratropium selective and specific, acting on the secretory function of the nasal mucosa.

Unusual extracranial complications of otitis media in a young HIV patient: retropharyngeal and Mouret's abscess.

Since the introduction of antibiotic therapy, the incidence of intra- and extracranial suppurative complication of acute and chronic purulent otitis media has sharply decreased. In particular, reports of laterocervical abscesses secondary to this disorder are quite rare, not more than twenty cases of Bezold's or Mouret's abscesses having been reported in the literature during the last ten years. The authors present a case of retropharyngeal and Mouret's abscess developed as a consequence of acute purulent otitis media in a young Aids patient. True otologic manifestations of Aids are rare while the incidental association of otologic disease with Aids is more common. The development of complication in the present case is favoured by the patients severe immunodepression.

[Surfactants of the airways. Critical review and personal research]. / Il surfattante delle vie aeree. Rassegna critica e ricerche personali.

The literature proving the presence of a surface tension lowering substance (STLS) on the lining layer of mammalian Eustachian tube (ET) is critically reviewed. A further review of the chemical studies on tubal washings based on chromatographic analysis methods (TLC and HPLC) is performed, and is concluded that ET epithelium is coated by a mixture of phospholipids, similar but not identical to the pulmonary surfactant and with similar but less powerful surface activity. In both cases, and with minor differences between the different mammalian species, phosphatidylcholine (PC), and in particular its disaturated fraction, dipalmitoilphosphatidylcholine (DPPC), is the predominating and the most active compound. ET surfactant is synthesized by ET epithelium and secreted in form of osmiophilic multilamellar bodies into the tubal lumen. The exact function of the ET surfactant is not fully understood: it may play an important role in ET physiology by facilitating the tubal opening to allow for aeration of the middle ear and adequate drainage or could act as a release agent, preventing solid-to-solid adhesion of the tubal walls and contrasting the adhesive action of the glycoproteins of the mucous blanket. On the other hand a phospholipidic surfactant seems to be produced by the mucosa of the other parts of the upper airways, i.e. nose and trachea. In this case a surface active agent could act in preventing the transudation of serum into the lumen, in enhancing the phagocytosis or in facilitating the mucociliary transport. Recent data on humans, suggesting that a relative deficiency or an alterated production of tubal surfactant could play a role in the pathogenesis of secretory otitis media (SOM) or middle ear effusion (MEE), are reviewed. Administration of exogenous surfactant or pharmacological stimulation of the production of tubal surfactant could improve ET function and be of value in some cases of SOM. Personal data, suggesting than ambroxol (a drug stimulating the production of pulmonary surfactant by the alveolar type II pneumocytes) exerts a similar activating effect on the tubotympanal secretory cells, are reported. These data support the results of clinical studies on the treatment of SOM with ambroxol.

Familial steatocystoma multiplex: HLA, Gm, Km genotyping and chromosomal analysis in two unrelated families.

Steatocystoma Multiplex (S.M.) is an inherited condition characterized by the appearance of cysts during the first or second decade of life. Familial cases have occasionally been reported. We studied 13 patients affected by S.M. from two unrelated families, focusing our attention on HLA, Gm and Km genotypes and on chromosomal analyses. Although we failed to correlate the syndrome with a particular HLA, Gm or Km haplotype, we report some peculiarities and differences between these two families and the healthy Italian population.

Recurrent extended HLA haplotypes in children with selective IgA deficiency.

HLA supratypes as well as serum IgG, IgA and IgM levels were determined in 44 children and adolescents with severe IgA deficiency (serum IgA less than 5 mg/dl) and in first degree relatives. Frequencies of the HLA alleles B14, DR1, DQW1, C4A2 and C4B2 were significantly higher in the IgA-deficient patients than in the controls. The most recurrent haplotype among patients was B14, DR1 (p less than 10(-4) preferentially associated with A33, A28 or A blank. The supratype B14, Bfs, C4A2, C4B2, DR1, DQW1 was present in a 14-fold higher frequency than in the controls, and strongly suggests the presence of a gene in the HLA region involved in the deficiency of IgA. The fact that this supratype was not always associated with IgA deficiency in the parents and that not all IgA-deficient subjects had this supratype is discussed. Severe IgA deficiency was found in four mothers (two of the four mother-child pairs shared the B14, DR1 haplotype); three other relatives (one father and two brothers) had partial IgA deficiency and did not have the B14, DR1, DQW1 haplotype.